Starting phenix.real_space_refine on Tue Feb 3 18:37:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.map" model { file = "/net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kye_62646/02_2026/9kye_62646.cif" } resolution = 2.61 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= 0.155 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 30 5.16 5 C 4003 2.51 5 N 1046 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6290 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1780 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Time building chain proxies: 1.05, per 1000 atoms: 0.17 Number of scatterers: 6290 At special positions: 0 Unit cell: (80.08, 80.08, 94.64, 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 30 16.00 O 1211 8.00 N 1046 7.00 C 4003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 110 " distance=2.03 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 110 " distance=2.04 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS G 47 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 110 " 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: 0.34 Conformation dependent library (CDL) restraints added in 307.5 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 24.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.660A pdb=" N ARG B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.705A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.836A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.613A pdb=" N VAL B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'C' and resid 58 through 73 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 73 Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'F' and resid 58 through 73 removed outlier: 3.859A pdb=" N GLU F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 58 through 73 Processing helix chain 'G' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 13 removed outlier: 3.867A pdb=" N LYS B 134 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG B 85 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE B 132 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLN B 133 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE B 154 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA B 135 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 152 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA B 137 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 24 removed outlier: 5.807A pdb=" N ILE C 16 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 35 " --> pdb=" O ILE C 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 49 current: chain 'C' and resid 98 through 106 removed outlier: 3.663A pdb=" N GLU C 109 " --> pdb=" O SER C 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 109 through 110 current: chain 'D' and resid 28 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 49 current: chain 'D' and resid 98 through 106 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 109 through 110 current: chain 'E' and resid 27 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 49 current: chain 'E' and resid 97 through 104 removed outlier: 8.759A pdb=" N VAL E 100 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN F 23 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE F 19 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE F 16 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 35 " --> pdb=" O ILE F 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 49 current: chain 'F' and resid 98 through 104 removed outlier: 8.820A pdb=" N VAL F 100 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN G 23 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE G 19 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE G 16 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL G 35 " --> pdb=" O ILE G 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 49 current: chain 'G' and resid 98 through 104 200 hydrogen bonds defined for protein. 555 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: 0.69 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1999 1.35 - 1.46: 1712 1.46 - 1.58: 2703 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 6451 Sorted by residual: bond pdb=" N VAL E 80 " pdb=" CA VAL E 80 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" CB PRO C 43 " pdb=" CG PRO C 43 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" CG PRO C 43 " pdb=" CD PRO C 43 " ideal model delta sigma weight residual 1.503 1.560 -0.057 3.40e-02 8.65e+02 2.78e+00 bond pdb=" C VAL E 80 " pdb=" O VAL E 80 " ideal model delta sigma weight residual 1.235 1.247 -0.012 9.90e-03 1.02e+04 1.54e+00 bond pdb=" CB ARG G 26 " pdb=" CG ARG G 26 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 ... (remaining 6446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8532 1.70 - 3.39: 178 3.39 - 5.09: 33 5.09 - 6.78: 4 6.78 - 8.48: 4 Bond angle restraints: 8751 Sorted by residual: angle pdb=" CA PRO C 43 " pdb=" N PRO C 43 " pdb=" CD PRO C 43 " ideal model delta sigma weight residual 112.00 104.55 7.45 1.40e+00 5.10e-01 2.83e+01 angle pdb=" C HIS B 72 " pdb=" N SER B 73 " pdb=" CA SER B 73 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CA ARG D 26 " pdb=" CB ARG D 26 " pdb=" CG ARG D 26 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG G 26 " pdb=" CB ARG G 26 " pdb=" CG ARG G 26 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 110.87 115.23 -4.36 1.54e+00 4.22e-01 8.03e+00 ... (remaining 8746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3190 17.69 - 35.37: 415 35.37 - 53.06: 166 53.06 - 70.75: 36 70.75 - 88.43: 11 Dihedral angle restraints: 3818 sinusoidal: 1480 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS D 105 " pdb=" SG CYS D 105 " pdb=" SG CYS D 110 " pdb=" CB CYS D 110 " ideal model delta sinusoidal sigma weight residual -86.00 -131.56 45.56 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CA CYS E 105 " pdb=" CB CYS E 105 " pdb=" SG CYS E 105 " pdb=" SG CYS E 110 " ideal model delta sinusoidal sigma weight residual 79.00 5.02 73.98 1 2.00e+01 2.50e-03 1.74e+01 dihedral pdb=" CA CYS C 105 " pdb=" CB CYS C 105 " pdb=" SG CYS C 105 " pdb=" SG CYS C 110 " ideal model delta sinusoidal sigma weight residual 79.00 8.63 70.37 1 2.00e+01 2.50e-03 1.59e+01 ... (remaining 3815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 526 0.032 - 0.064: 276 0.064 - 0.096: 90 0.096 - 0.128: 52 0.128 - 0.161: 6 Chirality restraints: 950 Sorted by residual: chirality pdb=" CB THR B 203 " pdb=" CA THR B 203 " pdb=" OG1 THR B 203 " pdb=" CG2 THR B 203 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE F 91 " pdb=" CA ILE F 91 " pdb=" CG1 ILE F 91 " pdb=" CG2 ILE F 91 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA LYS B 74 " pdb=" N LYS B 74 " pdb=" C LYS B 74 " pdb=" CB LYS B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 947 not shown) Planarity restraints: 1117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 42 " -0.067 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO C 43 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 42 " 0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO D 43 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 173 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO B 174 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.028 5.00e-02 4.00e+02 ... (remaining 1114 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 502 2.74 - 3.28: 6268 3.28 - 3.82: 11222 3.82 - 4.36: 14117 4.36 - 4.90: 23877 Nonbonded interactions: 55986 Sorted by model distance: nonbonded pdb=" N GLU D 40 " pdb=" OE1 GLU D 40 " model vdw 2.196 3.120 nonbonded pdb=" OE1 GLU C 64 " pdb=" NH1 ARG D 67 " model vdw 2.200 3.120 nonbonded pdb=" O ASN D 25 " pdb=" NH1 ARG D 26 " model vdw 2.210 3.120 nonbonded pdb=" O ASP G 52 " pdb=" OG SER G 53 " model vdw 2.223 3.040 nonbonded pdb=" NE2 GLN B 177 " pdb=" O ALA B 178 " model vdw 2.254 3.120 ... (remaining 55981 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.480 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.050 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.003 0.085 6462 Z= 0.148 Angle : 0.621 8.480 8773 Z= 0.354 Chirality : 0.047 0.161 950 Planarity : 0.006 0.097 1117 Dihedral : 19.011 88.433 2283 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.11 % Favored : 92.39 % Rotamer: Outliers : 5.77 % Allowed : 33.10 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.27), residues: 788 helix: -1.19 (0.37), residues: 170 sheet: 0.36 (0.30), residues: 235 loop : -2.08 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.015 0.001 TYR F 10 PHE 0.008 0.001 PHE F 30 TRP 0.009 0.001 TRP D 85 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6451) covalent geometry : angle 0.61975 ( 8751) SS BOND : bond 0.00199 ( 11) SS BOND : angle 1.02532 ( 22) hydrogen bonds : bond 0.17319 ( 200) hydrogen bonds : angle 8.21065 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.238 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 37 residues processed: 182 average time/residue: 0.4163 time to fit residues: 80.3962 Evaluate side-chains 176 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 86 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 87 ASN C 97 ASN F 74 HIS G 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114491 restraints weight = 7075.525| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.43 r_work: 0.3250 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6462 Z= 0.117 Angle : 0.552 6.916 8773 Z= 0.296 Chirality : 0.044 0.127 950 Planarity : 0.005 0.068 1117 Dihedral : 8.452 93.795 913 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.09 % Favored : 93.40 % Rotamer: Outliers : 6.20 % Allowed : 30.14 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 788 helix: -0.22 (0.38), residues: 174 sheet: 0.42 (0.29), residues: 235 loop : -2.03 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.010 0.001 TYR B 212 PHE 0.008 0.001 PHE C 30 TRP 0.008 0.001 TRP D 85 HIS 0.002 0.000 HIS G 20 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6451) covalent geometry : angle 0.55042 ( 8751) SS BOND : bond 0.00191 ( 11) SS BOND : angle 1.05718 ( 22) hydrogen bonds : bond 0.03663 ( 200) hydrogen bonds : angle 5.39059 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.304 Fit side-chains REVERT: B 61 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7304 (tppt) REVERT: B 182 GLN cc_start: 0.6500 (pt0) cc_final: 0.5969 (pp30) REVERT: B 198 TYR cc_start: 0.7835 (m-80) cc_final: 0.7583 (m-10) REVERT: C 10 TYR cc_start: 0.8320 (p90) cc_final: 0.8114 (p90) REVERT: C 92 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: E 54 LYS cc_start: 0.8778 (tmmm) cc_final: 0.8546 (tmmt) REVERT: F 62 MET cc_start: 0.8969 (tpp) cc_final: 0.8650 (mpp) REVERT: G 64 GLU cc_start: 0.7777 (tp30) cc_final: 0.7301 (tp30) REVERT: G 65 GLN cc_start: 0.8682 (tp40) cc_final: 0.7946 (tp40) outliers start: 44 outliers final: 20 residues processed: 182 average time/residue: 0.4776 time to fit residues: 91.9537 Evaluate side-chains 165 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 109 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 75 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 25 ASN C 87 ASN C 97 ASN F 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110203 restraints weight = 6942.898| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.43 r_work: 0.3193 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6462 Z= 0.160 Angle : 0.561 5.990 8773 Z= 0.301 Chirality : 0.046 0.153 950 Planarity : 0.004 0.059 1117 Dihedral : 6.426 57.555 880 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.09 % Favored : 93.40 % Rotamer: Outliers : 6.34 % Allowed : 29.72 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 788 helix: -0.05 (0.37), residues: 173 sheet: 0.36 (0.29), residues: 237 loop : -2.01 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 26 TYR 0.011 0.002 TYR C 11 PHE 0.010 0.001 PHE B 187 TRP 0.007 0.001 TRP F 2 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6451) covalent geometry : angle 0.55933 ( 8751) SS BOND : bond 0.00141 ( 11) SS BOND : angle 1.09661 ( 22) hydrogen bonds : bond 0.03473 ( 200) hydrogen bonds : angle 5.07639 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 61 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7400 (tptt) REVERT: B 83 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6764 (ttpt) REVERT: B 134 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7199 (ptpp) REVERT: B 182 GLN cc_start: 0.6435 (pt0) cc_final: 0.5952 (pp30) REVERT: C 71 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7772 (mp) REVERT: C 92 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: D 88 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7542 (tmmt) REVERT: E 36 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6903 (tmtm) REVERT: E 54 LYS cc_start: 0.8760 (tmmm) cc_final: 0.8492 (tmmt) REVERT: G 64 GLU cc_start: 0.7697 (tp30) cc_final: 0.7252 (tp30) outliers start: 45 outliers final: 24 residues processed: 172 average time/residue: 0.5245 time to fit residues: 95.0120 Evaluate side-chains 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN B 166 ASN B 181 GLN C 25 ASN C 87 ASN C 97 ASN F 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106810 restraints weight = 7056.938| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.44 r_work: 0.3139 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6462 Z= 0.211 Angle : 0.578 5.537 8773 Z= 0.312 Chirality : 0.047 0.147 950 Planarity : 0.005 0.054 1117 Dihedral : 5.979 53.275 874 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.35 % Favored : 93.15 % Rotamer: Outliers : 7.46 % Allowed : 28.87 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.27), residues: 788 helix: -0.03 (0.37), residues: 173 sheet: 0.28 (0.28), residues: 240 loop : -2.07 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 26 TYR 0.020 0.002 TYR B 63 PHE 0.014 0.001 PHE B 187 TRP 0.007 0.002 TRP F 2 HIS 0.006 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6451) covalent geometry : angle 0.57673 ( 8751) SS BOND : bond 0.00254 ( 11) SS BOND : angle 0.91953 ( 22) hydrogen bonds : bond 0.03671 ( 200) hydrogen bonds : angle 5.16692 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 61 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7313 (tptt) REVERT: B 134 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (ptpp) REVERT: B 182 GLN cc_start: 0.6389 (pt0) cc_final: 0.6075 (pp30) REVERT: B 212 TYR cc_start: 0.5603 (t80) cc_final: 0.5372 (t80) REVERT: C 71 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (mp) REVERT: D 88 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7176 (tmmt) REVERT: E 92 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: G 64 GLU cc_start: 0.7702 (tp30) cc_final: 0.7246 (tp30) outliers start: 53 outliers final: 27 residues processed: 174 average time/residue: 0.5487 time to fit residues: 100.2627 Evaluate side-chains 161 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN C 25 ASN C 87 ASN F 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108626 restraints weight = 7508.827| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.48 r_work: 0.3211 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6462 Z= 0.149 Angle : 0.548 6.997 8773 Z= 0.294 Chirality : 0.045 0.138 950 Planarity : 0.004 0.050 1117 Dihedral : 5.284 49.493 869 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.96 % Favored : 93.53 % Rotamer: Outliers : 5.35 % Allowed : 31.27 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 788 helix: 0.09 (0.36), residues: 173 sheet: 0.22 (0.29), residues: 237 loop : -2.05 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.015 0.001 TYR B 63 PHE 0.010 0.001 PHE B 187 TRP 0.009 0.001 TRP D 85 HIS 0.004 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6451) covalent geometry : angle 0.54772 ( 8751) SS BOND : bond 0.00178 ( 11) SS BOND : angle 0.60605 ( 22) hydrogen bonds : bond 0.03344 ( 200) hydrogen bonds : angle 4.95270 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.6876 (tpp-160) REVERT: B 47 SER cc_start: 0.8331 (m) cc_final: 0.8124 (p) REVERT: B 83 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6802 (ttpt) REVERT: B 182 GLN cc_start: 0.6310 (pt0) cc_final: 0.5796 (pp30) REVERT: C 14 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: C 71 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 26 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7257 (pmt-80) REVERT: D 88 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7081 (tmmt) REVERT: E 54 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8434 (tmmt) REVERT: G 64 GLU cc_start: 0.7549 (tp30) cc_final: 0.7313 (mm-30) outliers start: 38 outliers final: 24 residues processed: 162 average time/residue: 0.5380 time to fit residues: 91.6481 Evaluate side-chains 162 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN C 25 ASN C 87 ASN F 74 HIS G 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103099 restraints weight = 7087.546| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.50 r_work: 0.3084 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6462 Z= 0.260 Angle : 0.604 7.365 8773 Z= 0.326 Chirality : 0.049 0.143 950 Planarity : 0.005 0.049 1117 Dihedral : 5.530 52.061 868 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.22 % Favored : 93.27 % Rotamer: Outliers : 7.18 % Allowed : 28.87 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.27), residues: 788 helix: -0.01 (0.36), residues: 173 sheet: 0.17 (0.29), residues: 240 loop : -2.07 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 116 TYR 0.016 0.002 TYR B 198 PHE 0.014 0.001 PHE B 187 TRP 0.010 0.002 TRP F 2 HIS 0.004 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 6451) covalent geometry : angle 0.60414 ( 8751) SS BOND : bond 0.00227 ( 11) SS BOND : angle 0.58668 ( 22) hydrogen bonds : bond 0.03816 ( 200) hydrogen bonds : angle 5.19512 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6770 (ttpt) REVERT: B 116 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7721 (ttt180) REVERT: B 134 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7394 (pttp) REVERT: C 14 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: C 71 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7654 (mp) REVERT: D 88 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6945 (tmmt) REVERT: F 88 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7634 (mptt) REVERT: G 64 GLU cc_start: 0.7498 (tp30) cc_final: 0.7016 (tp30) REVERT: G 65 GLN cc_start: 0.8499 (tp40) cc_final: 0.7757 (tp40) REVERT: G 88 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7888 (tppp) outliers start: 51 outliers final: 28 residues processed: 171 average time/residue: 0.5634 time to fit residues: 101.1002 Evaluate side-chains 166 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 109 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 182 GLN C 87 ASN F 9 ASN F 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105903 restraints weight = 7520.941| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.53 r_work: 0.3197 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6462 Z= 0.153 Angle : 0.551 7.733 8773 Z= 0.298 Chirality : 0.046 0.161 950 Planarity : 0.004 0.047 1117 Dihedral : 5.177 47.418 868 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.22 % Favored : 93.27 % Rotamer: Outliers : 5.07 % Allowed : 30.99 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 788 helix: 0.06 (0.36), residues: 173 sheet: 0.15 (0.29), residues: 237 loop : -2.06 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 116 TYR 0.014 0.001 TYR B 63 PHE 0.010 0.001 PHE B 187 TRP 0.011 0.001 TRP D 85 HIS 0.004 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6451) covalent geometry : angle 0.55109 ( 8751) SS BOND : bond 0.00156 ( 11) SS BOND : angle 0.49729 ( 22) hydrogen bonds : bond 0.03389 ( 200) hydrogen bonds : angle 4.96045 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6519 (tptt) REVERT: B 83 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6801 (ttpt) REVERT: B 134 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7563 (pttp) REVERT: B 212 TYR cc_start: 0.5596 (t80) cc_final: 0.5316 (t80) REVERT: C 14 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: C 71 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7636 (mp) REVERT: D 88 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7010 (tmmt) REVERT: E 87 ASN cc_start: 0.7975 (t0) cc_final: 0.7523 (t0) REVERT: E 88 LYS cc_start: 0.8199 (tptm) cc_final: 0.7771 (tppt) REVERT: F 88 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7642 (mptt) REVERT: G 64 GLU cc_start: 0.7599 (tp30) cc_final: 0.7338 (mm-30) REVERT: G 65 GLN cc_start: 0.8559 (tp40) cc_final: 0.7862 (tp40) REVERT: G 88 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7997 (tppp) outliers start: 36 outliers final: 23 residues processed: 165 average time/residue: 0.5237 time to fit residues: 91.0964 Evaluate side-chains 165 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 61 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 182 GLN C 87 ASN F 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107405 restraints weight = 7560.221| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.54 r_work: 0.3217 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6462 Z= 0.131 Angle : 0.534 7.685 8773 Z= 0.288 Chirality : 0.045 0.159 950 Planarity : 0.004 0.046 1117 Dihedral : 5.025 44.217 868 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.47 % Favored : 93.15 % Rotamer: Outliers : 5.49 % Allowed : 30.85 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.27), residues: 788 helix: 0.18 (0.37), residues: 174 sheet: 0.17 (0.29), residues: 237 loop : -2.00 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 41 TYR 0.014 0.001 TYR B 63 PHE 0.009 0.001 PHE B 187 TRP 0.011 0.001 TRP D 85 HIS 0.004 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6451) covalent geometry : angle 0.53428 ( 8751) SS BOND : bond 0.00141 ( 11) SS BOND : angle 0.48671 ( 22) hydrogen bonds : bond 0.03243 ( 200) hydrogen bonds : angle 4.80257 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 47 SER cc_start: 0.8355 (m) cc_final: 0.8078 (p) REVERT: B 61 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6514 (tptt) REVERT: B 83 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6786 (ttpt) REVERT: B 182 GLN cc_start: 0.6543 (pt0) cc_final: 0.6303 (pt0) REVERT: B 202 GLN cc_start: 0.7706 (mm110) cc_final: 0.7419 (mm-40) REVERT: B 212 TYR cc_start: 0.5460 (t80) cc_final: 0.5210 (t80) REVERT: C 14 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: C 71 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7649 (mp) REVERT: D 88 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7013 (tmmt) REVERT: E 87 ASN cc_start: 0.7960 (t0) cc_final: 0.7530 (t0) REVERT: E 88 LYS cc_start: 0.8222 (tptm) cc_final: 0.7804 (tppt) REVERT: F 88 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7611 (mptt) REVERT: G 64 GLU cc_start: 0.7587 (tp30) cc_final: 0.7349 (mm-30) REVERT: G 88 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7998 (tppp) outliers start: 39 outliers final: 20 residues processed: 167 average time/residue: 0.5312 time to fit residues: 93.3327 Evaluate side-chains 161 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 10.0000 chunk 51 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 87 ASN F 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105228 restraints weight = 7645.065| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.55 r_work: 0.3189 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6462 Z= 0.195 Angle : 0.579 7.798 8773 Z= 0.312 Chirality : 0.047 0.159 950 Planarity : 0.004 0.047 1117 Dihedral : 4.830 43.213 866 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.60 % Favored : 93.15 % Rotamer: Outliers : 4.79 % Allowed : 30.99 % Favored : 64.23 % 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: -1.24 (0.27), residues: 788 helix: 0.16 (0.37), residues: 173 sheet: 0.14 (0.29), residues: 240 loop : -2.00 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.021 0.002 TYR B 158 PHE 0.011 0.001 PHE B 187 TRP 0.008 0.002 TRP D 85 HIS 0.004 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6451) covalent geometry : angle 0.57935 ( 8751) SS BOND : bond 0.00162 ( 11) SS BOND : angle 0.44270 ( 22) hydrogen bonds : bond 0.03518 ( 200) hydrogen bonds : angle 4.91081 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6479 (tptt) REVERT: B 83 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6765 (ttpt) REVERT: B 182 GLN cc_start: 0.6461 (pt0) cc_final: 0.6199 (pt0) REVERT: B 212 TYR cc_start: 0.5481 (t80) cc_final: 0.5235 (t80) REVERT: C 14 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: C 71 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7665 (mp) REVERT: D 88 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6992 (tmmt) REVERT: E 87 ASN cc_start: 0.7962 (t0) cc_final: 0.7535 (t0) REVERT: E 88 LYS cc_start: 0.8242 (tptm) cc_final: 0.7819 (tppt) REVERT: F 88 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7617 (mptt) REVERT: G 64 GLU cc_start: 0.7520 (tp30) cc_final: 0.7277 (mm-30) REVERT: G 88 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8004 (tppp) outliers start: 34 outliers final: 22 residues processed: 161 average time/residue: 0.5151 time to fit residues: 87.2859 Evaluate side-chains 161 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 104 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 50 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN C 87 ASN F 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108570 restraints weight = 7479.996| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.54 r_work: 0.3236 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6462 Z= 0.126 Angle : 0.550 8.061 8773 Z= 0.296 Chirality : 0.045 0.158 950 Planarity : 0.004 0.045 1117 Dihedral : 4.617 39.977 866 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.60 % Favored : 93.15 % Rotamer: Outliers : 3.94 % Allowed : 31.97 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.27), residues: 788 helix: 0.30 (0.37), residues: 174 sheet: 0.11 (0.29), residues: 237 loop : -1.96 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.017 0.001 TYR B 63 PHE 0.009 0.001 PHE B 187 TRP 0.013 0.001 TRP D 85 HIS 0.004 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6451) covalent geometry : angle 0.55008 ( 8751) SS BOND : bond 0.00142 ( 11) SS BOND : angle 0.53274 ( 22) hydrogen bonds : bond 0.03282 ( 200) hydrogen bonds : angle 4.76087 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: B 41 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7259 (tpp-160) REVERT: B 47 SER cc_start: 0.8324 (m) cc_final: 0.8060 (p) REVERT: B 61 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6463 (tptt) REVERT: B 85 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7778 (ttp-170) REVERT: B 134 LYS cc_start: 0.7710 (pttp) cc_final: 0.7504 (pttm) REVERT: B 212 TYR cc_start: 0.5229 (t80) cc_final: 0.5010 (t80) REVERT: C 64 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7473 (pt0) REVERT: C 71 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7621 (mp) REVERT: C 92 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7469 (mm-30) REVERT: D 64 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: D 88 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6992 (tmmt) REVERT: E 87 ASN cc_start: 0.7944 (t0) cc_final: 0.7548 (t0) REVERT: E 88 LYS cc_start: 0.8234 (tptm) cc_final: 0.7814 (tppt) REVERT: F 88 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7583 (mptt) REVERT: G 64 GLU cc_start: 0.7673 (tp30) cc_final: 0.7440 (mm-30) REVERT: G 88 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7998 (tppp) outliers start: 28 outliers final: 21 residues processed: 163 average time/residue: 0.5173 time to fit residues: 88.8205 Evaluate side-chains 163 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 71 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN C 25 ASN C 65 GLN C 87 ASN C 97 ASN F 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107419 restraints weight = 7587.285| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.56 r_work: 0.3223 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6462 Z= 0.146 Angle : 0.569 7.956 8773 Z= 0.307 Chirality : 0.046 0.154 950 Planarity : 0.004 0.045 1117 Dihedral : 4.435 39.467 865 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.47 % Favored : 93.27 % Rotamer: Outliers : 3.94 % Allowed : 31.97 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.27), residues: 788 helix: 0.33 (0.37), residues: 174 sheet: 0.17 (0.29), residues: 238 loop : -1.95 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 116 TYR 0.029 0.001 TYR B 158 PHE 0.009 0.001 PHE B 187 TRP 0.010 0.001 TRP D 85 HIS 0.004 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6451) covalent geometry : angle 0.56896 ( 8751) SS BOND : bond 0.00149 ( 11) SS BOND : angle 0.38903 ( 22) hydrogen bonds : bond 0.03392 ( 200) hydrogen bonds : angle 4.78667 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.48 seconds wall clock time: 48 minutes 56.97 seconds (2936.97 seconds total)