Starting phenix.real_space_refine on Sun Mar 10 19:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9k_36110/03_2024/8j9k_36110.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 14 5.16 5 C 2727 2.51 5 N 744 2.21 5 O 799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4284 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2542 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 785 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 957 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.77, per 1000 atoms: 0.65 Number of scatterers: 4284 At special positions: 0 Unit cell: (70.3779, 107.419, 106.184, 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 14 16.00 O 799 8.00 N 744 7.00 C 2727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 112 " distance=2.04 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 823.5 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.4% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.965A pdb=" N LEU C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 113 through 117 Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.547A pdb=" N GLY C 40 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 7 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 391 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL C 9 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.687A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 16.110A pdb=" N GLN C 173 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 20.660A pdb=" N CYS C 141 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 144 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL C 56 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.687A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 16.110A pdb=" N GLN C 173 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 20.660A pdb=" N CYS C 141 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 131 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 289 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 187 through 190 removed outlier: 3.514A pdb=" N THR C 187 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 201 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 223 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 211 removed outlier: 6.365A pdb=" N TYR C 210 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 323 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 345 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N VAL C 321 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 211 removed outlier: 6.365A pdb=" N TYR C 210 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 323 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 345 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N VAL C 321 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 232 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 233 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 260 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.560A pdb=" N THR B 96 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.814A pdb=" N ALA B 108 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 57 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR B 73 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP B 59 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.814A pdb=" N ALA B 108 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.553A pdb=" N CYS D 48 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 105 " --> pdb=" O CYS D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 86 removed outlier: 6.837A pdb=" N TRP D 62 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 76 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 60 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 139 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 86 removed outlier: 6.837A pdb=" N TRP D 62 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 76 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 60 " --> pdb=" O SER D 76 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1401 1.34 - 1.46: 1030 1.46 - 1.58: 1931 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 4380 Sorted by residual: bond pdb=" C ASP C 136 " pdb=" N THR C 137 " ideal model delta sigma weight residual 1.331 1.277 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" N GLN B 113 " pdb=" CA GLN B 113 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.67e+00 bond pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.22e-02 6.72e+03 3.37e+00 bond pdb=" CA VAL C 316 " pdb=" CB VAL C 316 " ideal model delta sigma weight residual 1.542 1.521 0.021 1.33e-02 5.65e+03 2.49e+00 bond pdb=" CA VAL C 273 " pdb=" CB VAL C 273 " ideal model delta sigma weight residual 1.544 1.521 0.023 1.46e-02 4.69e+03 2.41e+00 ... (remaining 4375 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.31: 136 106.31 - 113.22: 2379 113.22 - 120.13: 1384 120.13 - 127.04: 2032 127.04 - 133.95: 50 Bond angle restraints: 5981 Sorted by residual: angle pdb=" CA GLN C 131 " pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 119.06 112.37 6.69 1.05e+00 9.07e-01 4.06e+01 angle pdb=" O GLN C 131 " pdb=" C GLN C 131 " pdb=" N PRO C 132 " ideal model delta sigma weight residual 121.23 128.12 -6.89 1.13e+00 7.83e-01 3.72e+01 angle pdb=" C GLN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 120.03 114.14 5.89 9.90e-01 1.02e+00 3.54e+01 angle pdb=" C SER B 74 " pdb=" N ALA B 75 " pdb=" CA ALA B 75 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA GLN B 113 " pdb=" C GLN B 113 " pdb=" O GLN B 113 " ideal model delta sigma weight residual 120.66 116.66 4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 5976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2342 17.71 - 35.42: 190 35.42 - 53.13: 54 53.13 - 70.84: 13 70.84 - 88.55: 5 Dihedral angle restraints: 2604 sinusoidal: 889 harmonic: 1715 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 112 " pdb=" CB CYS B 112 " ideal model delta sinusoidal sigma weight residual 93.00 35.49 57.51 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA TYR D 128 " pdb=" C TYR D 128 " pdb=" N TYR D 129 " pdb=" CA TYR D 129 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C GLN B 113 " pdb=" N GLN B 113 " pdb=" CA GLN B 113 " pdb=" CB GLN B 113 " ideal model delta harmonic sigma weight residual -122.60 -113.19 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 547 0.051 - 0.101: 112 0.101 - 0.151: 35 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLN B 113 " pdb=" N GLN B 113 " pdb=" C GLN B 113 " pdb=" CB GLN B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL C 339 " pdb=" N VAL C 339 " pdb=" C VAL C 339 " pdb=" CB VAL C 339 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL C 331 " pdb=" CA VAL C 331 " pdb=" CG1 VAL C 331 " pdb=" CG2 VAL C 331 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 693 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 132 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C TYR D 132 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR D 132 " -0.016 2.00e-02 2.50e+03 pdb=" N MET D 133 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 240 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR C 240 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR C 240 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 240 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 240 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 240 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 240 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 240 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 182 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 183 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " 0.022 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 917 2.78 - 3.31: 4008 3.31 - 3.84: 6709 3.84 - 4.37: 7482 4.37 - 4.90: 13639 Nonbonded interactions: 32755 Sorted by model distance: nonbonded pdb=" NH2 ARG B 42 " pdb=" OG1 THR B 44 " model vdw 2.247 2.520 nonbonded pdb=" NH1 ARG D 64 " pdb=" OD1 ASP D 116 " model vdw 2.299 2.520 nonbonded pdb=" OE1 GLN D 108 " pdb=" ND2 ASN D 110 " model vdw 2.318 2.520 nonbonded pdb=" N GLU D 32 " pdb=" OE1 GLU D 32 " model vdw 2.318 2.520 nonbonded pdb=" O GLY C 133 " pdb=" N ASP C 136 " model vdw 2.359 2.520 ... (remaining 32750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 3.730 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.055 4380 Z= 0.299 Angle : 0.763 9.204 5981 Z= 0.417 Chirality : 0.046 0.252 696 Planarity : 0.005 0.040 774 Dihedral : 15.318 88.546 1496 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.95 % Allowed : 19.05 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.34), residues: 582 helix: -3.14 (1.02), residues: 17 sheet: -1.19 (0.31), residues: 263 loop : -1.82 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS C 114 PHE 0.012 0.002 PHE C 76 TYR 0.037 0.002 TYR C 240 ARG 0.004 0.001 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.538 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.1570 time to fit residues: 14.3904 Evaluate side-chains 51 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4380 Z= 0.249 Angle : 0.636 8.458 5981 Z= 0.318 Chirality : 0.045 0.158 696 Planarity : 0.005 0.039 774 Dihedral : 4.769 27.466 638 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.57 % Allowed : 19.52 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.33), residues: 582 helix: -2.94 (0.92), residues: 23 sheet: -0.97 (0.31), residues: 258 loop : -1.86 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 62 HIS 0.002 0.001 HIS C 114 PHE 0.010 0.001 PHE C 118 TYR 0.014 0.002 TYR C 240 ARG 0.002 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 71 LEU cc_start: 0.8343 (tp) cc_final: 0.8142 (mp) REVERT: B 103 GLN cc_start: 0.7085 (mm110) cc_final: 0.6790 (mm110) REVERT: B 118 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6970 (m-30) outliers start: 15 outliers final: 7 residues processed: 71 average time/residue: 0.1498 time to fit residues: 13.9341 Evaluate side-chains 65 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 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 114 HIS C 123 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4380 Z= 0.220 Angle : 0.600 8.137 5981 Z= 0.299 Chirality : 0.043 0.154 696 Planarity : 0.005 0.066 774 Dihedral : 4.565 27.615 638 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 4.05 % Allowed : 19.52 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.33), residues: 582 helix: -2.64 (1.01), residues: 23 sheet: -0.81 (0.31), residues: 260 loop : -1.80 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 62 HIS 0.002 0.001 HIS C 114 PHE 0.008 0.001 PHE C 117 TYR 0.014 0.002 TYR C 240 ARG 0.005 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8690 (m-40) cc_final: 0.8380 (m-40) REVERT: C 122 GLN cc_start: 0.8000 (pm20) cc_final: 0.6977 (pt0) REVERT: C 298 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 63 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8537 (mmmm) REVERT: B 118 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: D 128 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.6722 (m-80) outliers start: 17 outliers final: 12 residues processed: 72 average time/residue: 0.1495 time to fit residues: 14.4152 Evaluate side-chains 67 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4380 Z= 0.291 Angle : 0.598 6.002 5981 Z= 0.302 Chirality : 0.043 0.153 696 Planarity : 0.005 0.053 774 Dihedral : 4.625 27.826 638 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 4.76 % Allowed : 20.24 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.33), residues: 582 helix: -2.71 (0.97), residues: 23 sheet: -0.85 (0.31), residues: 266 loop : -1.80 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 73 HIS 0.004 0.001 HIS C 114 PHE 0.009 0.001 PHE C 117 TYR 0.013 0.002 TYR C 240 ARG 0.002 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8720 (m-40) cc_final: 0.8468 (m-40) REVERT: C 122 GLN cc_start: 0.8024 (pm20) cc_final: 0.7333 (pt0) REVERT: C 298 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: B 63 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8500 (mmmm) REVERT: B 118 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: D 128 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7315 (m-80) outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.1266 time to fit residues: 11.5107 Evaluate side-chains 67 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4380 Z= 0.184 Angle : 0.549 6.022 5981 Z= 0.276 Chirality : 0.042 0.146 696 Planarity : 0.004 0.044 774 Dihedral : 4.342 28.301 638 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.30 % Rotamer: Outliers : 5.24 % Allowed : 20.95 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.33), residues: 582 helix: -2.40 (1.05), residues: 23 sheet: -0.67 (0.31), residues: 268 loop : -1.64 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 140 HIS 0.005 0.001 HIS C 347 PHE 0.008 0.001 PHE C 116 TYR 0.014 0.001 TYR B 73 ARG 0.001 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8705 (m-40) cc_final: 0.8440 (m-40) REVERT: C 122 GLN cc_start: 0.8006 (pm20) cc_final: 0.7238 (pt0) REVERT: C 289 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7999 (pp) REVERT: C 298 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 63 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8618 (mmmm) REVERT: D 128 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7392 (m-80) outliers start: 22 outliers final: 12 residues processed: 74 average time/residue: 0.1399 time to fit residues: 13.8484 Evaluate side-chains 64 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.230 Angle : 0.565 7.340 5981 Z= 0.284 Chirality : 0.043 0.190 696 Planarity : 0.004 0.036 774 Dihedral : 4.387 28.646 638 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.87 % Favored : 92.96 % Rotamer: Outliers : 5.48 % Allowed : 20.71 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.34), residues: 582 helix: -2.35 (1.03), residues: 23 sheet: -0.65 (0.31), residues: 269 loop : -1.64 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 59 HIS 0.006 0.001 HIS C 347 PHE 0.009 0.001 PHE C 117 TYR 0.014 0.001 TYR B 73 ARG 0.008 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8741 (m-40) cc_final: 0.8497 (m-40) REVERT: C 122 GLN cc_start: 0.8007 (pm20) cc_final: 0.7255 (pt0) REVERT: C 289 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8006 (pp) REVERT: C 298 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: B 63 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8602 (mmmm) REVERT: D 128 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7431 (m-80) outliers start: 23 outliers final: 15 residues processed: 72 average time/residue: 0.1290 time to fit residues: 12.7200 Evaluate side-chains 67 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.229 Angle : 0.555 6.544 5981 Z= 0.281 Chirality : 0.043 0.178 696 Planarity : 0.004 0.037 774 Dihedral : 4.379 28.518 638 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.87 % Favored : 92.96 % Rotamer: Outliers : 6.19 % Allowed : 20.95 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.34), residues: 582 helix: -2.55 (0.97), residues: 23 sheet: -0.54 (0.32), residues: 267 loop : -1.60 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS C 114 PHE 0.009 0.001 PHE C 117 TYR 0.014 0.001 TYR B 73 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 54 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8776 (m-40) cc_final: 0.8561 (m-40) REVERT: C 122 GLN cc_start: 0.8100 (pm20) cc_final: 0.7393 (pt0) REVERT: C 298 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: B 63 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8588 (mmmm) REVERT: D 128 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7513 (m-80) outliers start: 26 outliers final: 19 residues processed: 75 average time/residue: 0.1314 time to fit residues: 13.2780 Evaluate side-chains 73 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.0970 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4380 Z= 0.161 Angle : 0.562 8.443 5981 Z= 0.273 Chirality : 0.043 0.156 696 Planarity : 0.004 0.036 774 Dihedral : 4.168 28.521 638 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 5.48 % Allowed : 22.14 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.34), residues: 582 helix: -2.24 (1.02), residues: 23 sheet: -0.38 (0.32), residues: 266 loop : -1.50 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 140 HIS 0.003 0.000 HIS C 114 PHE 0.008 0.001 PHE C 116 TYR 0.014 0.001 TYR B 73 ARG 0.008 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: C 16 ASN cc_start: 0.8767 (m-40) cc_final: 0.8564 (m-40) REVERT: C 122 GLN cc_start: 0.7988 (pm20) cc_final: 0.7250 (pt0) REVERT: C 298 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 63 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8561 (mmmm) REVERT: D 128 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7288 (m-80) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 0.1273 time to fit residues: 13.2200 Evaluate side-chains 72 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.195 Angle : 0.574 7.804 5981 Z= 0.278 Chirality : 0.043 0.155 696 Planarity : 0.004 0.036 774 Dihedral : 4.193 27.945 638 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.81 % Rotamer: Outliers : 5.48 % Allowed : 22.86 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.34), residues: 582 helix: -2.16 (1.03), residues: 23 sheet: -0.33 (0.32), residues: 265 loop : -1.54 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 59 HIS 0.003 0.000 HIS C 114 PHE 0.009 0.001 PHE C 116 TYR 0.020 0.001 TYR C 240 ARG 0.008 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 122 GLN cc_start: 0.7954 (pm20) cc_final: 0.7214 (pt0) REVERT: C 298 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: B 63 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8551 (mmmm) REVERT: D 128 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7348 (m-80) outliers start: 23 outliers final: 18 residues processed: 73 average time/residue: 0.1278 time to fit residues: 12.4897 Evaluate side-chains 71 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN C 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4380 Z= 0.283 Angle : 0.605 7.972 5981 Z= 0.297 Chirality : 0.044 0.184 696 Planarity : 0.004 0.043 774 Dihedral : 4.386 28.019 638 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.70 % Favored : 93.13 % Rotamer: Outliers : 5.24 % Allowed : 23.10 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.34), residues: 582 helix: -2.17 (1.02), residues: 23 sheet: -0.40 (0.32), residues: 266 loop : -1.59 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 59 HIS 0.003 0.001 HIS C 114 PHE 0.009 0.001 PHE C 117 TYR 0.019 0.002 TYR C 240 ARG 0.010 0.001 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.503 Fit side-chains REVERT: C 122 GLN cc_start: 0.7969 (pm20) cc_final: 0.7249 (pt0) REVERT: C 298 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: B 63 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8568 (mmmm) REVERT: D 128 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7425 (m-80) outliers start: 22 outliers final: 18 residues processed: 72 average time/residue: 0.1172 time to fit residues: 11.9025 Evaluate side-chains 68 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.116341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093588 restraints weight = 9642.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094411 restraints weight = 5751.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094900 restraints weight = 4797.365| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4380 Z= 0.221 Angle : 0.585 7.994 5981 Z= 0.285 Chirality : 0.043 0.156 696 Planarity : 0.004 0.041 774 Dihedral : 4.329 28.274 638 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 5.00 % Allowed : 24.05 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 582 helix: -2.04 (1.06), residues: 23 sheet: -0.38 (0.32), residues: 268 loop : -1.58 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 59 HIS 0.004 0.001 HIS C 114 PHE 0.009 0.001 PHE C 116 TYR 0.017 0.001 TYR C 240 ARG 0.010 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1234.67 seconds wall clock time: 23 minutes 0.53 seconds (1380.53 seconds total)