Starting phenix.real_space_refine on Tue Aug 4 22:11:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zfy_74165/08_2026/9zfy_74165.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4313 2.51 5 N 1158 2.21 5 O 1360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6857 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 206} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 206} Chain: "J" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 219 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 8, 'TRANS': 22} Chain: "G" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1614 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1618 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 203} Chain breaks: 1 Time building chain proxies: 1.78, per 1000 atoms: 0.26 Number of scatterers: 6857 At special positions: 0 Unit cell: (71.8, 75.39, 147.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1360 8.00 N 1158 7.00 C 4313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 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: 0.56 Conformation dependent library (CDL) restraints added in 352.8 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 20 sheets defined 9.5% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.612A pdb=" N VAL D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.589A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N ASN J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 52A through 54 removed outlier: 3.588A pdb=" N GLY G 54 " --> pdb=" O LYS G 52B" (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.571A pdb=" N ASP G 86 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR G 87 " --> pdb=" O THR G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 52A through 54 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.613A pdb=" N THR C 87 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.244A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.834A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.799A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.054A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 150 Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.158A pdb=" N ALA G 33 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.016A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG G 94 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.748A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.748A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.166A pdb=" N ALA C 33 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.074A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.074A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 169 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 154 303 hydrogen bonds defined for protein. 708 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: 1.10 Time building geometry restraints manager: 0.74 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: 2210 1.34 - 1.46: 1663 1.46 - 1.58: 3109 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 7016 Sorted by residual: bond pdb=" N ASN J 1 " pdb=" CA ASN J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N GLU C 1 " pdb=" CA GLU C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N GLU G 1 " pdb=" CA GLU G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 7011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 8965 1.07 - 2.15: 429 2.15 - 3.22: 75 3.22 - 4.29: 68 4.29 - 5.37: 12 Bond angle restraints: 9549 Sorted by residual: angle pdb=" CA ARG D 91 " pdb=" CB ARG D 91 " pdb=" CG ARG D 91 " ideal model delta sigma weight residual 114.10 119.47 -5.37 2.00e+00 2.50e-01 7.20e+00 angle pdb=" C ASN J 15 " pdb=" CA ASN J 15 " pdb=" CB ASN J 15 " ideal model delta sigma weight residual 116.34 112.80 3.54 1.40e+00 5.10e-01 6.39e+00 angle pdb=" CG ARG C 19 " pdb=" CD ARG C 19 " pdb=" NE ARG C 19 " ideal model delta sigma weight residual 112.00 117.13 -5.13 2.20e+00 2.07e-01 5.44e+00 angle pdb=" CB GLU H 143 " pdb=" CG GLU H 143 " pdb=" CD GLU H 143 " ideal model delta sigma weight residual 112.60 116.53 -3.93 1.70e+00 3.46e-01 5.34e+00 angle pdb=" CB LYS C 43 " pdb=" CG LYS C 43 " pdb=" CD LYS C 43 " ideal model delta sigma weight residual 111.30 116.48 -5.18 2.30e+00 1.89e-01 5.07e+00 ... (remaining 9544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3921 17.93 - 35.87: 217 35.87 - 53.80: 53 53.80 - 71.74: 11 71.74 - 89.67: 9 Dihedral angle restraints: 4211 sinusoidal: 1622 harmonic: 2589 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 54.75 38.25 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS H 134 " pdb=" SG CYS H 134 " pdb=" SG CYS H 194 " pdb=" CB CYS H 194 " ideal model delta sinusoidal sigma weight residual 93.00 62.25 30.75 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB GLU D 165 " pdb=" CG GLU D 165 " pdb=" CD GLU D 165 " pdb=" OE1 GLU D 165 " ideal model delta sinusoidal sigma weight residual 0.00 89.56 -89.56 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 580 0.030 - 0.059: 331 0.059 - 0.089: 77 0.089 - 0.119: 67 0.119 - 0.148: 18 Chirality restraints: 1073 Sorted by residual: chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA VAL H 132 " pdb=" N VAL H 132 " pdb=" C VAL H 132 " pdb=" CB VAL H 132 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 1070 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 148 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO G 149 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 149 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 201 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 202 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 77 " 0.132 9.50e-02 1.11e+02 5.97e-02 2.71e+00 pdb=" NE ARG D 77 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 77 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 77 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 77 " 0.001 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 73 2.65 - 3.21: 6084 3.21 - 3.77: 9993 3.77 - 4.34: 14724 4.34 - 4.90: 24789 Nonbonded interactions: 55663 Sorted by model distance: nonbonded pdb=" OD1 ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.083 3.040 nonbonded pdb=" OD1 ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.127 3.040 nonbonded pdb=" OD2 ASP G 72 " pdb=" NZ LYS G 75 " model vdw 2.223 3.120 nonbonded pdb=" OG SER H 121 " pdb=" O PRO G 123 " model vdw 2.245 3.040 nonbonded pdb=" N GLU G 6 " pdb=" OE1 GLU G 6 " model vdw 2.248 3.120 ... (remaining 55658 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 'C' and (resid 1 through 133 or resid 135 through 213)) 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: 6.360 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.004 0.033 7024 Z= 0.151 Angle : 0.629 5.367 9565 Z= 0.321 Chirality : 0.046 0.148 1073 Planarity : 0.005 0.060 1233 Dihedral : 12.906 89.669 2533 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.22 (0.29), residues: 888 helix: -1.42 (0.94), residues: 34 sheet: 0.34 (0.26), residues: 381 loop : 0.25 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 19 TYR 0.012 0.001 TYR H 32 PHE 0.012 0.001 PHE H 71 TRP 0.014 0.001 TRP H 148 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7016) covalent geometry : angle 0.62905 / 0.32 ( 9549) SS BOND : bond 0.00342 / 0.19 ( 8) SS BOND : angle 0.80727 / 0.48 ( 16) hydrogen bonds : bond 0.13350 / 9.14 ( 272) hydrogen bonds : angle 7.30945 / 5.12 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.287 Fit side-chains REVERT: H 61 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7893 (ptt-90) REVERT: H 76 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7754 (mtp-110) REVERT: H 89 MET cc_start: 0.8338 (ttt) cc_final: 0.7969 (ttt) REVERT: H 105 GLU cc_start: 0.8052 (pm20) cc_final: 0.7839 (pt0) REVERT: H 132 VAL cc_start: 0.8790 (t) cc_final: 0.8545 (p) REVERT: H 165 GLU cc_start: 0.8229 (mp0) cc_final: 0.7896 (mp0) REVERT: D 74 LYS cc_start: 0.8041 (mttt) cc_final: 0.7433 (mtpp) REVERT: D 123 GLU cc_start: 0.7439 (mp0) cc_final: 0.6911 (mp0) REVERT: G 43 LYS cc_start: 0.8433 (mmtp) cc_final: 0.7750 (mtmt) REVERT: G 59 TYR cc_start: 0.9177 (m-80) cc_final: 0.8868 (m-80) REVERT: G 74 SER cc_start: 0.8571 (p) cc_final: 0.8268 (m) REVERT: C 6 GLU cc_start: 0.8767 (mp0) cc_final: 0.8554 (mp0) REVERT: C 75 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8513 (mtmm) REVERT: C 82 SER cc_start: 0.9023 (m) cc_final: 0.8670 (t) REVERT: C 182 VAL cc_start: 0.8618 (p) cc_final: 0.8304 (m) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1249 time to fit residues: 16.7884 Evaluate side-chains 94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 137 ASN H 189 HIS D 27EASN D 147 GLN D 160 GLN C 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111319 restraints weight = 8793.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109922 restraints weight = 8764.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110919 restraints weight = 8379.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111101 restraints weight = 6547.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111225 restraints weight = 5981.833| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7024 Z= 0.178 Angle : 0.556 5.943 9565 Z= 0.290 Chirality : 0.043 0.164 1073 Planarity : 0.005 0.061 1233 Dihedral : 4.345 17.998 967 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.39 % Allowed : 4.25 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.35 (0.29), residues: 888 helix: -1.35 (1.06), residues: 28 sheet: 0.45 (0.26), residues: 386 loop : 0.28 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.012 0.002 TYR H 49 PHE 0.013 0.001 PHE D 139 TRP 0.009 0.001 TRP G 47 HIS 0.004 0.001 HIS H 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 7016) covalent geometry : angle 0.55469 / 0.29 ( 9549) SS BOND : bond 0.00318 / 0.18 ( 8) SS BOND : angle 0.97663 / 0.62 ( 16) hydrogen bonds : bond 0.03177 / 2.20 ( 272) hydrogen bonds : angle 6.13645 / 4.35 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.263 Fit side-chains REVERT: H 124 GLN cc_start: 0.9011 (tt0) cc_final: 0.8754 (tt0) REVERT: H 165 GLU cc_start: 0.7870 (mp0) cc_final: 0.7668 (mp0) REVERT: D 90 GLN cc_start: 0.9264 (pp30) cc_final: 0.8798 (pp30) REVERT: G 43 LYS cc_start: 0.8505 (mmtp) cc_final: 0.7989 (mtmt) REVERT: G 59 TYR cc_start: 0.9106 (m-80) cc_final: 0.8874 (m-80) REVERT: C 75 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8483 (mtmm) outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.1238 time to fit residues: 16.4953 Evaluate side-chains 87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain D residue 12 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 27EASN D 147 GLN D 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113650 restraints weight = 8687.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112099 restraints weight = 8674.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112664 restraints weight = 9076.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113034 restraints weight = 7026.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113203 restraints weight = 6256.580| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7024 Z= 0.113 Angle : 0.504 5.503 9565 Z= 0.261 Chirality : 0.042 0.139 1073 Planarity : 0.004 0.046 1233 Dihedral : 4.097 16.959 967 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.77 % Allowed : 8.12 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.53 (0.29), residues: 888 helix: -1.17 (1.07), residues: 28 sheet: 0.61 (0.26), residues: 370 loop : 0.37 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.013 0.001 TYR D 140 PHE 0.007 0.001 PHE H 71 TRP 0.005 0.001 TRP C 103 HIS 0.002 0.001 HIS G 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7016) covalent geometry : angle 0.50400 / 0.26 ( 9549) SS BOND : bond 0.00294 / 0.16 ( 8) SS BOND : angle 0.70521 / 0.42 ( 16) hydrogen bonds : bond 0.02794 / 1.91 ( 272) hydrogen bonds : angle 5.71425 / 4.06 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.262 Fit side-chains REVERT: H 124 GLN cc_start: 0.8897 (tt0) cc_final: 0.8663 (tt0) REVERT: D 90 GLN cc_start: 0.9050 (pp30) cc_final: 0.8739 (pp30) REVERT: D 123 GLU cc_start: 0.7845 (mp0) cc_final: 0.7313 (mp0) REVERT: D 142 ARG cc_start: 0.8152 (tmm-80) cc_final: 0.7765 (ptm160) REVERT: J 13 ASN cc_start: 0.8323 (t0) cc_final: 0.7923 (p0) REVERT: G 43 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8011 (mtmt) REVERT: C 75 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8484 (mttm) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.1128 time to fit residues: 13.9900 Evaluate side-chains 87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 27EASN D 100 GLN D 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111268 restraints weight = 8792.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109619 restraints weight = 9066.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110479 restraints weight = 8856.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110765 restraints weight = 6840.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110910 restraints weight = 6234.728| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7024 Z= 0.136 Angle : 0.510 6.312 9565 Z= 0.263 Chirality : 0.042 0.192 1073 Planarity : 0.004 0.053 1233 Dihedral : 4.066 15.742 967 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.68 % Allowed : 8.76 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.50 (0.29), residues: 888 helix: -1.17 (1.05), residues: 28 sheet: 0.56 (0.26), residues: 377 loop : 0.38 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 77 TYR 0.016 0.001 TYR D 140 PHE 0.009 0.001 PHE D 139 TRP 0.006 0.001 TRP G 47 HIS 0.002 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7016) covalent geometry : angle 0.50920 / 0.26 ( 9549) SS BOND : bond 0.00295 / 0.17 ( 8) SS BOND : angle 0.69027 / 0.45 ( 16) hydrogen bonds : bond 0.02762 / 1.89 ( 272) hydrogen bonds : angle 5.61701 / 3.99 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.266 Fit side-chains REVERT: D 90 GLN cc_start: 0.9185 (pp30) cc_final: 0.8810 (pp30) REVERT: D 123 GLU cc_start: 0.7923 (mp0) cc_final: 0.7526 (mp0) REVERT: D 142 ARG cc_start: 0.8129 (tmm-80) cc_final: 0.7746 (ptm160) REVERT: J 13 ASN cc_start: 0.8332 (t0) cc_final: 0.7934 (p0) REVERT: G 43 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8056 (mtmt) REVERT: C 75 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8455 (mttm) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1026 time to fit residues: 12.2320 Evaluate side-chains 91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 124 GLN D 27EASN D 100 GLN D 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107882 restraints weight = 8907.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106839 restraints weight = 8859.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107342 restraints weight = 8843.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107774 restraints weight = 7147.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107945 restraints weight = 6185.365| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7024 Z= 0.205 Angle : 0.550 6.016 9565 Z= 0.285 Chirality : 0.043 0.188 1073 Planarity : 0.004 0.048 1233 Dihedral : 4.328 15.691 967 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 9.02 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.34 (0.28), residues: 888 helix: -1.33 (1.03), residues: 28 sheet: 0.50 (0.26), residues: 377 loop : 0.23 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 77 TYR 0.022 0.002 TYR D 140 PHE 0.012 0.001 PHE D 139 TRP 0.010 0.001 TRP G 47 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 7016) covalent geometry : angle 0.54948 / 0.28 ( 9549) SS BOND : bond 0.00344 / 0.21 ( 8) SS BOND : angle 0.76697 / 0.53 ( 16) hydrogen bonds : bond 0.03080 / 2.11 ( 272) hydrogen bonds : angle 5.90337 / 4.20 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.245 Fit side-chains REVERT: D 90 GLN cc_start: 0.9263 (pp30) cc_final: 0.8861 (pp30) REVERT: D 123 GLU cc_start: 0.7964 (mp0) cc_final: 0.7609 (mp0) REVERT: J 13 ASN cc_start: 0.8425 (t0) cc_final: 0.7962 (p0) REVERT: G 43 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8076 (mtmt) REVERT: G 75 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7837 (ptmt) REVERT: C 75 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8492 (mttm) outliers start: 18 outliers final: 10 residues processed: 106 average time/residue: 0.1098 time to fit residues: 14.9056 Evaluate side-chains 94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 124 GLN H 137 ASN D 27EASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107240 restraints weight = 8957.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.106856 restraints weight = 7004.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107207 restraints weight = 6165.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107831 restraints weight = 5496.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107997 restraints weight = 4882.206| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7024 Z= 0.220 Angle : 0.558 5.080 9565 Z= 0.290 Chirality : 0.043 0.158 1073 Planarity : 0.005 0.051 1233 Dihedral : 4.379 15.431 967 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.45 % Allowed : 10.31 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.18 (0.28), residues: 888 helix: -1.38 (1.03), residues: 28 sheet: 0.39 (0.26), residues: 391 loop : 0.11 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.025 0.002 TYR D 140 PHE 0.013 0.002 PHE D 139 TRP 0.009 0.001 TRP G 47 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 ( 7016) covalent geometry : angle 0.55783 / 0.29 ( 9549) SS BOND : bond 0.00343 / 0.18 ( 8) SS BOND : angle 0.75208 / 0.53 ( 16) hydrogen bonds : bond 0.03129 / 2.13 ( 272) hydrogen bonds : angle 5.98235 / 4.26 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: D 90 GLN cc_start: 0.9254 (pp30) cc_final: 0.8827 (pp30) REVERT: D 123 GLU cc_start: 0.7979 (mp0) cc_final: 0.7735 (mt-10) REVERT: D 142 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7797 (ptm160) REVERT: D 145 LYS cc_start: 0.7900 (tptm) cc_final: 0.7647 (mmmt) REVERT: J 13 ASN cc_start: 0.8460 (t0) cc_final: 0.8052 (p0) REVERT: G 43 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8087 (mtmt) REVERT: C 75 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8470 (mttm) outliers start: 19 outliers final: 14 residues processed: 108 average time/residue: 0.1254 time to fit residues: 16.9229 Evaluate side-chains 101 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 124 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109157 restraints weight = 8861.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107944 restraints weight = 9157.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108488 restraints weight = 9363.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108709 restraints weight = 7219.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108984 restraints weight = 6600.834| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7024 Z= 0.155 Angle : 0.525 4.788 9565 Z= 0.271 Chirality : 0.042 0.145 1073 Planarity : 0.004 0.047 1233 Dihedral : 4.219 14.981 967 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.80 % Allowed : 10.95 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.27 (0.29), residues: 888 helix: -1.32 (1.05), residues: 28 sheet: 0.39 (0.26), residues: 393 loop : 0.23 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.019 0.001 TYR D 140 PHE 0.016 0.001 PHE D 209 TRP 0.006 0.001 TRP G 103 HIS 0.002 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 7016) covalent geometry : angle 0.52461 / 0.27 ( 9549) SS BOND : bond 0.00290 / 0.16 ( 8) SS BOND : angle 0.62355 / 0.42 ( 16) hydrogen bonds : bond 0.02910 / 2.00 ( 272) hydrogen bonds : angle 5.78944 / 4.12 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: D 90 GLN cc_start: 0.9221 (pp30) cc_final: 0.8748 (pp30) REVERT: D 123 GLU cc_start: 0.8007 (mp0) cc_final: 0.7764 (mt-10) REVERT: D 145 LYS cc_start: 0.7862 (tptm) cc_final: 0.7633 (mmmt) REVERT: D 162 SER cc_start: 0.9079 (t) cc_final: 0.8664 (m) REVERT: J 13 ASN cc_start: 0.8454 (t0) cc_final: 0.8112 (p0) REVERT: G 43 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8085 (mtmt) REVERT: C 25 SER cc_start: 0.8829 (t) cc_final: 0.8443 (m) REVERT: C 75 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8439 (mttm) outliers start: 14 outliers final: 13 residues processed: 103 average time/residue: 0.1183 time to fit residues: 15.4192 Evaluate side-chains 100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 124 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108176 restraints weight = 8926.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107045 restraints weight = 9199.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107534 restraints weight = 9034.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107788 restraints weight = 7568.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108074 restraints weight = 6649.158| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7024 Z= 0.142 Angle : 0.517 4.650 9565 Z= 0.267 Chirality : 0.042 0.140 1073 Planarity : 0.004 0.049 1233 Dihedral : 4.140 14.404 967 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.32 % Allowed : 11.08 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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 (0.29), residues: 888 helix: -1.22 (1.07), residues: 28 sheet: 0.46 (0.26), residues: 389 loop : 0.33 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 77 TYR 0.018 0.001 TYR D 140 PHE 0.013 0.001 PHE D 209 TRP 0.006 0.001 TRP G 103 HIS 0.002 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7016) covalent geometry : angle 0.51665 / 0.27 ( 9549) SS BOND : bond 0.00271 / 0.14 ( 8) SS BOND : angle 0.61903 / 0.41 ( 16) hydrogen bonds : bond 0.02789 / 1.90 ( 272) hydrogen bonds : angle 5.66932 / 4.04 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: D 90 GLN cc_start: 0.9098 (pp30) cc_final: 0.8798 (pp30) REVERT: D 123 GLU cc_start: 0.8052 (mp0) cc_final: 0.7780 (mt-10) REVERT: D 145 LYS cc_start: 0.7797 (tptm) cc_final: 0.7580 (mmmt) REVERT: J 13 ASN cc_start: 0.8425 (t0) cc_final: 0.8135 (p0) REVERT: G 43 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8093 (mtmt) REVERT: C 75 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8435 (mttm) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.1162 time to fit residues: 14.5488 Evaluate side-chains 100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 124 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109428 restraints weight = 8868.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108100 restraints weight = 8957.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108695 restraints weight = 9312.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108977 restraints weight = 7270.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109259 restraints weight = 6453.628| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7024 Z= 0.113 Angle : 0.500 4.904 9565 Z= 0.257 Chirality : 0.041 0.134 1073 Planarity : 0.004 0.056 1233 Dihedral : 4.046 14.126 967 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 11.60 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.48 (0.29), residues: 888 helix: -1.16 (1.08), residues: 28 sheet: 0.53 (0.26), residues: 394 loop : 0.37 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 77 TYR 0.016 0.001 TYR D 140 PHE 0.012 0.001 PHE D 209 TRP 0.005 0.001 TRP G 154 HIS 0.001 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7016) covalent geometry : angle 0.50024 / 0.26 ( 9549) SS BOND : bond 0.00244 / 0.12 ( 8) SS BOND : angle 0.56053 / 0.36 ( 16) hydrogen bonds : bond 0.02663 / 1.83 ( 272) hydrogen bonds : angle 5.50996 / 3.92 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: D 90 GLN cc_start: 0.9153 (pp30) cc_final: 0.8724 (pp30) REVERT: D 123 GLU cc_start: 0.8058 (mp0) cc_final: 0.7768 (mt-10) REVERT: D 145 LYS cc_start: 0.7816 (tptm) cc_final: 0.7599 (mmmt) REVERT: J 13 ASN cc_start: 0.8387 (t0) cc_final: 0.8142 (p0) REVERT: G 43 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8119 (mtmt) REVERT: G 58 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7509 (mt-10) REVERT: C 25 SER cc_start: 0.8881 (t) cc_final: 0.8529 (m) REVERT: C 75 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8438 (mttm) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1125 time to fit residues: 13.9626 Evaluate side-chains 94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109495 restraints weight = 8831.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108449 restraints weight = 9035.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109198 restraints weight = 8744.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109434 restraints weight = 6838.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109581 restraints weight = 6285.382| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7024 Z= 0.115 Angle : 0.503 5.408 9565 Z= 0.258 Chirality : 0.041 0.136 1073 Planarity : 0.005 0.059 1233 Dihedral : 4.013 13.767 967 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.42 % Allowed : 12.50 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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: 0.53 (0.29), residues: 888 helix: -1.07 (1.09), residues: 28 sheet: 0.57 (0.25), residues: 394 loop : 0.39 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 77 TYR 0.017 0.001 TYR D 140 PHE 0.017 0.001 PHE D 209 TRP 0.005 0.001 TRP G 103 HIS 0.001 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7016) covalent geometry : angle 0.50315 / 0.26 ( 9549) SS BOND : bond 0.00243 / 0.12 ( 8) SS BOND : angle 0.56507 / 0.36 ( 16) hydrogen bonds : bond 0.02650 / 1.81 ( 272) hydrogen bonds : angle 5.46209 / 3.89 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.263 Fit side-chains REVERT: D 90 GLN cc_start: 0.9110 (pp30) cc_final: 0.8831 (pp30) REVERT: D 123 GLU cc_start: 0.8042 (mp0) cc_final: 0.7754 (mt-10) REVERT: D 145 LYS cc_start: 0.7807 (tptm) cc_final: 0.7593 (mmmt) REVERT: J 13 ASN cc_start: 0.8386 (t0) cc_final: 0.8123 (p0) REVERT: G 43 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8124 (mtmt) REVERT: C 25 SER cc_start: 0.8900 (t) cc_final: 0.8530 (m) REVERT: C 75 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8433 (mttm) outliers start: 11 outliers final: 11 residues processed: 93 average time/residue: 0.1116 time to fit residues: 13.3886 Evaluate side-chains 91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 27EASN D 100 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107537 restraints weight = 8825.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106222 restraints weight = 9430.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106968 restraints weight = 10197.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107598 restraints weight = 7918.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107897 restraints weight = 6551.201| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7024 Z= 0.157 Angle : 0.521 5.062 9565 Z= 0.269 Chirality : 0.042 0.140 1073 Planarity : 0.005 0.055 1233 Dihedral : 4.137 14.044 967 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 12.50 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % 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 (0.29), residues: 888 helix: -1.00 (1.08), residues: 28 sheet: 0.50 (0.25), residues: 394 loop : 0.37 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 77 TYR 0.019 0.001 TYR D 140 PHE 0.011 0.001 PHE D 209 TRP 0.006 0.001 TRP G 103 HIS 0.002 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7016) covalent geometry : angle 0.52067 / 0.27 ( 9549) SS BOND : bond 0.00262 / 0.14 ( 8) SS BOND : angle 0.60778 / 0.43 ( 16) hydrogen bonds : bond 0.02825 / 1.93 ( 272) hydrogen bonds : angle 5.64033 / 4.00 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.48 seconds wall clock time: 23 minutes 36.24 seconds (1416.24 seconds total)