Starting phenix.real_space_refine on Tue Feb 3 16:42:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubq_64014/02_2026/9ubq_64014.map" } resolution = 2.86 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= 0.017 sd= 0.086 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 32 5.16 5 C 3164 2.51 5 N 854 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 5020 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 775 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 786 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "B" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 775 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "F" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 786 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 1.42, per 1000 atoms: 0.28 Number of scatterers: 5020 At special positions: 0 Unit cell: (97.461, 67.473, 113.288, 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 32 16.00 O 970 8.00 N 854 7.00 C 3164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 138 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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: 0.41 Conformation dependent library (CDL) restraints added in 475.6 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 22.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 73 through 101 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.505A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.966A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 73 through 101 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.505A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.966A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 8.585A pdb=" N THR B 126 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS A 141 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 151 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.298A pdb=" N TYR C 33 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP C 34 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.672A pdb=" N CYS C 95 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TRP C 111 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG C 97 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR C 107 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.272A pdb=" N VAL D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.297A pdb=" N TYR E 33 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP E 34 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.674A pdb=" N CYS E 95 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP E 111 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG E 97 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYR E 107 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.272A pdb=" N VAL F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N HIS F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 642 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: 0.80 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1433 1.33 - 1.46: 1132 1.46 - 1.58: 2537 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 5142 Sorted by residual: bond pdb=" CA TYR C 107 " pdb=" C TYR C 107 " ideal model delta sigma weight residual 1.523 1.489 0.035 1.19e-02 7.06e+03 8.45e+00 bond pdb=" CA TYR E 107 " pdb=" C TYR E 107 " ideal model delta sigma weight residual 1.523 1.490 0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N TYR C 107 " pdb=" CA TYR C 107 " ideal model delta sigma weight residual 1.454 1.432 0.022 1.18e-02 7.18e+03 3.39e+00 bond pdb=" N TYR E 107 " pdb=" CA TYR E 107 " ideal model delta sigma weight residual 1.454 1.432 0.022 1.18e-02 7.18e+03 3.33e+00 bond pdb=" C TYR E 107 " pdb=" O TYR E 107 " ideal model delta sigma weight residual 1.234 1.211 0.023 1.28e-02 6.10e+03 3.30e+00 ... (remaining 5137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 6765 1.26 - 2.53: 185 2.53 - 3.79: 50 3.79 - 5.05: 6 5.05 - 6.32: 6 Bond angle restraints: 7012 Sorted by residual: angle pdb=" N ASN C 31 " pdb=" CA ASN C 31 " pdb=" CB ASN C 31 " ideal model delta sigma weight residual 113.65 110.18 3.47 1.47e+00 4.63e-01 5.57e+00 angle pdb=" N ASN E 31 " pdb=" CA ASN E 31 " pdb=" CB ASN E 31 " ideal model delta sigma weight residual 113.65 110.18 3.47 1.47e+00 4.63e-01 5.57e+00 angle pdb=" CA TYR C 107 " pdb=" C TYR C 107 " pdb=" N PHE C 108 " ideal model delta sigma weight residual 115.27 118.38 -3.11 1.47e+00 4.63e-01 4.47e+00 angle pdb=" CA TYR E 107 " pdb=" C TYR E 107 " pdb=" N PHE E 108 " ideal model delta sigma weight residual 115.27 118.37 -3.10 1.47e+00 4.63e-01 4.43e+00 angle pdb=" CA TYR E 107 " pdb=" C TYR E 107 " pdb=" O TYR E 107 " ideal model delta sigma weight residual 121.56 119.05 2.51 1.21e+00 6.83e-01 4.30e+00 ... (remaining 7007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 2759 14.97 - 29.93: 212 29.93 - 44.89: 75 44.89 - 59.86: 10 59.86 - 74.82: 8 Dihedral angle restraints: 3064 sinusoidal: 1118 harmonic: 1946 Sorted by residual: dihedral pdb=" CB CYS A 124 " pdb=" SG CYS A 124 " pdb=" SG CYS A 137 " pdb=" CB CYS A 137 " ideal model delta sinusoidal sigma weight residual -86.00 -135.41 49.41 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS B 124 " pdb=" SG CYS B 124 " pdb=" SG CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sinusoidal sigma weight residual -86.00 -135.26 49.26 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 65.21 27.79 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 3061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 511 0.031 - 0.063: 196 0.063 - 0.094: 40 0.094 - 0.126: 34 0.126 - 0.157: 9 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA ILE E 37 " pdb=" N ILE E 37 " pdb=" C ILE E 37 " pdb=" CB ILE E 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA ILE C 37 " pdb=" N ILE C 37 " pdb=" C ILE C 37 " pdb=" CB ILE C 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CB ILE B 150 " pdb=" CA ILE B 150 " pdb=" CG1 ILE B 150 " pdb=" CG2 ILE B 150 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 787 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 106 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C ASN E 106 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN E 106 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR E 107 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 106 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" C ASN C 106 " 0.019 2.00e-02 2.50e+03 pdb=" O ASN C 106 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR C 107 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 153 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.014 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1206 2.79 - 3.32: 4545 3.32 - 3.85: 8654 3.85 - 4.37: 10305 4.37 - 4.90: 17972 Nonbonded interactions: 42682 Sorted by model distance: nonbonded pdb=" OG SER E 35 " pdb=" NE2 HIS E 98 " model vdw 2.263 3.120 nonbonded pdb=" OG SER C 35 " pdb=" NE2 HIS C 98 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP B 144 " pdb=" OH TYR E 107 " model vdw 2.308 3.040 nonbonded pdb=" OD1 ASP A 144 " pdb=" OH TYR C 107 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR C 68 " pdb=" NH1 ARG C 83 " model vdw 2.371 3.120 ... (remaining 42677 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.240 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.760 Find NCS groups from input model: 0.040 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.035 5154 Z= 0.173 Angle : 0.562 6.318 7036 Z= 0.292 Chirality : 0.041 0.157 790 Planarity : 0.004 0.033 894 Dihedral : 12.594 74.823 1780 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.34), residues: 662 helix: 4.48 (0.40), residues: 112 sheet: -0.32 (0.33), residues: 226 loop : 0.24 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 97 TYR 0.007 0.001 TYR C 94 PHE 0.013 0.001 PHE A 161 TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5142) covalent geometry : angle 0.55950 ( 7012) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.11047 ( 24) hydrogen bonds : bond 0.08655 ( 240) hydrogen bonds : angle 5.93608 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3839 time to fit residues: 33.7329 Evaluate side-chains 78 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN C 115 ASN B 146 ASN E 115 ASN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110935 restraints weight = 5890.483| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.18 r_work: 0.3169 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5154 Z= 0.151 Angle : 0.520 5.465 7036 Z= 0.261 Chirality : 0.041 0.139 790 Planarity : 0.004 0.027 894 Dihedral : 4.008 15.383 722 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.13 % Allowed : 8.83 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.38 (0.34), residues: 662 helix: 4.53 (0.40), residues: 112 sheet: 0.43 (0.36), residues: 192 loop : 0.06 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.009 0.001 TYR E 94 PHE 0.016 0.001 PHE A 161 TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5142) covalent geometry : angle 0.51743 ( 7012) SS BOND : bond 0.00336 ( 12) SS BOND : angle 1.07147 ( 24) hydrogen bonds : bond 0.02428 ( 240) hydrogen bonds : angle 5.03136 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.172 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.3905 time to fit residues: 38.2710 Evaluate side-chains 94 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115612 restraints weight = 5853.759| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.07 r_work: 0.3234 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5154 Z= 0.098 Angle : 0.468 5.509 7036 Z= 0.233 Chirality : 0.040 0.137 790 Planarity : 0.004 0.026 894 Dihedral : 3.765 15.568 722 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.50 % Allowed : 13.91 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.55 (0.34), residues: 662 helix: 4.64 (0.39), residues: 112 sheet: 0.63 (0.37), residues: 192 loop : 0.12 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.008 0.001 TYR C 94 PHE 0.008 0.001 PHE A 161 TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5142) covalent geometry : angle 0.46578 ( 7012) SS BOND : bond 0.00246 ( 12) SS BOND : angle 0.83626 ( 24) hydrogen bonds : bond 0.02012 ( 240) hydrogen bonds : angle 4.52298 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.137 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.4593 time to fit residues: 40.3784 Evaluate side-chains 85 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN D 27 GLN E 115 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109395 restraints weight = 5851.368| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.15 r_work: 0.3144 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5154 Z= 0.182 Angle : 0.515 5.481 7036 Z= 0.260 Chirality : 0.041 0.142 790 Planarity : 0.004 0.034 894 Dihedral : 3.977 15.701 722 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.26 % Allowed : 14.66 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.34), residues: 662 helix: 4.67 (0.39), residues: 112 sheet: 0.59 (0.37), residues: 192 loop : 0.07 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 122 TYR 0.012 0.001 TYR C 107 PHE 0.014 0.001 PHE A 161 TRP 0.009 0.001 TRP C 47 HIS 0.004 0.002 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5142) covalent geometry : angle 0.51174 ( 7012) SS BOND : bond 0.00427 ( 12) SS BOND : angle 1.05431 ( 24) hydrogen bonds : bond 0.02405 ( 240) hydrogen bonds : angle 4.66779 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.195 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.5029 time to fit residues: 43.9937 Evaluate side-chains 87 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111349 restraints weight = 5893.955| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.09 r_work: 0.3172 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5154 Z= 0.148 Angle : 0.498 5.467 7036 Z= 0.249 Chirality : 0.040 0.139 790 Planarity : 0.004 0.026 894 Dihedral : 3.902 15.895 722 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.01 % Allowed : 14.29 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.54 (0.34), residues: 662 helix: 4.75 (0.39), residues: 112 sheet: 0.64 (0.37), residues: 192 loop : 0.06 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 122 TYR 0.009 0.001 TYR C 94 PHE 0.012 0.001 PHE B 161 TRP 0.008 0.001 TRP C 47 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5142) covalent geometry : angle 0.49550 ( 7012) SS BOND : bond 0.00385 ( 12) SS BOND : angle 0.98038 ( 24) hydrogen bonds : bond 0.02231 ( 240) hydrogen bonds : angle 4.56710 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.141 Fit side-chains REVERT: D 70 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7853 (tm-30) REVERT: F 70 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7849 (tm-30) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.4749 time to fit residues: 41.1738 Evaluate side-chains 88 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 0.0870 chunk 52 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 65 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115115 restraints weight = 5937.517| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.09 r_work: 0.3227 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5154 Z= 0.097 Angle : 0.463 5.457 7036 Z= 0.230 Chirality : 0.039 0.136 790 Planarity : 0.004 0.025 894 Dihedral : 3.678 15.852 722 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.07 % Allowed : 15.60 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.34), residues: 662 helix: 4.85 (0.38), residues: 112 sheet: 0.75 (0.37), residues: 192 loop : 0.13 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.008 0.001 TYR C 94 PHE 0.010 0.001 PHE A 161 TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5142) covalent geometry : angle 0.46130 ( 7012) SS BOND : bond 0.00270 ( 12) SS BOND : angle 0.81509 ( 24) hydrogen bonds : bond 0.01924 ( 240) hydrogen bonds : angle 4.29712 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.238 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.5185 time to fit residues: 47.8000 Evaluate side-chains 89 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN D 27 GLN E 115 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112094 restraints weight = 5824.337| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.07 r_work: 0.3180 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5154 Z= 0.154 Angle : 0.495 5.457 7036 Z= 0.248 Chirality : 0.040 0.140 790 Planarity : 0.004 0.025 894 Dihedral : 3.837 15.748 722 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.76 % Allowed : 15.41 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.61 (0.34), residues: 662 helix: 4.79 (0.39), residues: 112 sheet: 0.70 (0.37), residues: 192 loop : 0.10 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.010 0.001 TYR C 94 PHE 0.012 0.001 PHE A 161 TRP 0.008 0.001 TRP C 47 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5142) covalent geometry : angle 0.49249 ( 7012) SS BOND : bond 0.00374 ( 12) SS BOND : angle 0.93493 ( 24) hydrogen bonds : bond 0.02182 ( 240) hydrogen bonds : angle 4.47786 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.193 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 0.4571 time to fit residues: 42.1905 Evaluate side-chains 92 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 115 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111350 restraints weight = 5885.642| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.09 r_work: 0.3175 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5154 Z= 0.159 Angle : 0.505 5.532 7036 Z= 0.252 Chirality : 0.040 0.138 790 Planarity : 0.004 0.025 894 Dihedral : 3.897 15.685 722 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.20 % Allowed : 16.17 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.55 (0.34), residues: 662 helix: 4.75 (0.38), residues: 112 sheet: 0.48 (0.37), residues: 198 loop : 0.17 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 38 TYR 0.010 0.001 TYR C 94 PHE 0.013 0.001 PHE A 161 TRP 0.007 0.001 TRP E 47 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5142) covalent geometry : angle 0.50213 ( 7012) SS BOND : bond 0.00395 ( 12) SS BOND : angle 1.01411 ( 24) hydrogen bonds : bond 0.02229 ( 240) hydrogen bonds : angle 4.52217 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.218 Fit side-chains REVERT: D 105 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7731 (mt-10) REVERT: F 105 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7755 (mt-10) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.5176 time to fit residues: 47.5872 Evaluate side-chains 93 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 115 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111294 restraints weight = 5874.263| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.10 r_work: 0.3172 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5154 Z= 0.158 Angle : 0.507 5.560 7036 Z= 0.254 Chirality : 0.040 0.139 790 Planarity : 0.004 0.038 894 Dihedral : 3.922 15.665 722 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.57 % Allowed : 16.17 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.53 (0.34), residues: 662 helix: 4.77 (0.38), residues: 112 sheet: 0.47 (0.37), residues: 198 loop : 0.14 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.010 0.001 TYR C 94 PHE 0.013 0.001 PHE A 161 TRP 0.007 0.001 TRP C 47 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5142) covalent geometry : angle 0.50440 ( 7012) SS BOND : bond 0.00390 ( 12) SS BOND : angle 1.04511 ( 24) hydrogen bonds : bond 0.02234 ( 240) hydrogen bonds : angle 4.53189 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.197 Fit side-chains REVERT: D 105 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7727 (mt-10) REVERT: F 105 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7727 (mt-10) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.5286 time to fit residues: 48.0888 Evaluate side-chains 94 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110654 restraints weight = 5846.759| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.08 r_work: 0.3161 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5154 Z= 0.175 Angle : 0.521 5.941 7036 Z= 0.262 Chirality : 0.041 0.140 790 Planarity : 0.004 0.039 894 Dihedral : 3.995 15.435 722 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.01 % Allowed : 16.92 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.48 (0.34), residues: 662 helix: 4.72 (0.38), residues: 112 sheet: 0.45 (0.37), residues: 198 loop : 0.11 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 122 TYR 0.010 0.001 TYR C 94 PHE 0.014 0.001 PHE A 161 TRP 0.007 0.001 TRP C 47 HIS 0.005 0.002 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5142) covalent geometry : angle 0.51841 ( 7012) SS BOND : bond 0.00418 ( 12) SS BOND : angle 1.06279 ( 24) hydrogen bonds : bond 0.02341 ( 240) hydrogen bonds : angle 4.61171 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.190 Fit side-chains REVERT: D 105 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7718 (mt-10) REVERT: F 105 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7741 (mt-10) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.5323 time to fit residues: 46.6730 Evaluate side-chains 93 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 chunk 47 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.0000 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 115 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112775 restraints weight = 5927.144| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.08 r_work: 0.3191 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5154 Z= 0.133 Angle : 0.494 5.782 7036 Z= 0.247 Chirality : 0.040 0.137 790 Planarity : 0.004 0.037 894 Dihedral : 3.867 15.831 722 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 17.29 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.55 (0.34), residues: 662 helix: 4.78 (0.38), residues: 112 sheet: 0.51 (0.37), residues: 198 loop : 0.13 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 122 TYR 0.010 0.001 TYR C 94 PHE 0.012 0.001 PHE A 161 TRP 0.006 0.001 TRP E 47 HIS 0.003 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5142) covalent geometry : angle 0.49163 ( 7012) SS BOND : bond 0.00336 ( 12) SS BOND : angle 0.98854 ( 24) hydrogen bonds : bond 0.02081 ( 240) hydrogen bonds : angle 4.46743 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.72 seconds wall clock time: 37 minutes 19.94 seconds (2239.94 seconds total)