Starting phenix.real_space_refine on Sat May 10 02:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.map" model { file = "/net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8za6_39874/05_2025/8za6_39874.cif" } resolution = 3.43 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= -0.001 sd= 0.061 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 36 5.16 5 C 3032 2.51 5 N 746 2.21 5 O 855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 891 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "g" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "m" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.78 Number of scatterers: 4669 At special positions: 0 Unit cell: (75.9, 92.4, 104.5, 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 36 16.00 O 855 8.00 N 746 7.00 C 3032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.04 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.04 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " 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: 1.11 Conformation dependent library (CDL) restraints added in 563.2 milliseconds 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 10 sheets defined 41.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'a' and resid 32 through 54 removed outlier: 3.663A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR a 42 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY a 43 " --> pdb=" O LEU a 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 53 removed outlier: 3.965A pdb=" N ASP b 36 " --> pdb=" O CYS b 32 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY b 37 " --> pdb=" O TYR b 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR b 42 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU b 51 " --> pdb=" O THR b 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 66 Processing helix chain 'd' and resid 100 through 127 removed outlier: 3.661A pdb=" N PHE d 125 " --> pdb=" O GLY d 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.535A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 104 through 108' Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.981A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 153 through 155 No H-bonds generated for 'chain 'e' and resid 153 through 155' Processing helix chain 'f' and resid 126 through 156 Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 113 through 138 removed outlier: 3.547A pdb=" N ALA g 137 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY g 138 " --> pdb=" O TYR g 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 258 through 289 removed outlier: 3.708A pdb=" N MET m 262 " --> pdb=" O LYS m 258 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU m 267 " --> pdb=" O SER m 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY m 268 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA m 274 " --> pdb=" O ARG m 270 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS m 275 " --> pdb=" O MET m 271 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS m 286 " --> pdb=" O LEU m 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU m 287 " --> pdb=" O LEU m 283 " (cutoff:3.500A) Processing helix chain 'n' and resid 283 through 320 removed outlier: 3.521A pdb=" N LEU n 288 " --> pdb=" O LEU n 284 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR n 289 " --> pdb=" O LEU n 285 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER n 304 " --> pdb=" O LEU n 300 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL n 305 " --> pdb=" O LEU n 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL n 306 " --> pdb=" O LEU n 302 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR n 307 " --> pdb=" O LYS n 303 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS n 314 " --> pdb=" O ILE n 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'd' and resid 43 through 46 removed outlier: 5.849A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE d 70 " --> pdb=" O GLU d 45 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN e 60 " --> pdb=" O VAL e 97 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.930A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.703A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR f 44 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 58 through 59 Processing sheet with id=AA7, first strand: chain 'f' and resid 94 through 96 removed outlier: 3.761A pdb=" N GLY f 94 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU f 112 " --> pdb=" O TYR f 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.786A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 54 through 56 removed outlier: 7.172A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 636 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: 1.16 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1450 1.35 - 1.46: 1125 1.46 - 1.58: 2131 1.58 - 1.70: 3 1.70 - 1.82: 49 Bond restraints: 4758 Sorted by residual: bond pdb=" CB PRO b 29 " pdb=" CG PRO b 29 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" C CYS f 49 " pdb=" N PRO f 50 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 bond pdb=" CB PRO d 25 " pdb=" CG PRO d 25 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.91e+00 bond pdb=" CB PRO e 105 " pdb=" CG PRO e 105 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.48e+00 bond pdb=" C23 CLR b 201 " pdb=" C24 CLR b 201 " ideal model delta sigma weight residual 1.525 1.490 0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 4753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 6375 3.27 - 6.53: 70 6.53 - 9.80: 8 9.80 - 13.07: 5 13.07 - 16.33: 1 Bond angle restraints: 6459 Sorted by residual: angle pdb=" CA PRO b 29 " pdb=" N PRO b 29 " pdb=" CD PRO b 29 " ideal model delta sigma weight residual 112.00 95.67 16.33 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO e 105 " pdb=" N PRO e 105 " pdb=" CD PRO e 105 " ideal model delta sigma weight residual 112.00 104.17 7.83 1.40e+00 5.10e-01 3.13e+01 angle pdb=" N PRO b 29 " pdb=" CD PRO b 29 " pdb=" CG PRO b 29 " ideal model delta sigma weight residual 103.20 96.01 7.19 1.50e+00 4.44e-01 2.29e+01 angle pdb=" CA PRO d 25 " pdb=" N PRO d 25 " pdb=" CD PRO d 25 " ideal model delta sigma weight residual 112.00 105.78 6.22 1.40e+00 5.10e-01 1.98e+01 angle pdb=" CB LYS f 153 " pdb=" CG LYS f 153 " pdb=" CD LYS f 153 " ideal model delta sigma weight residual 111.30 120.33 -9.03 2.30e+00 1.89e-01 1.54e+01 ... (remaining 6454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 2295 15.90 - 31.80: 402 31.80 - 47.70: 149 47.70 - 63.60: 40 63.60 - 79.50: 6 Dihedral angle restraints: 2892 sinusoidal: 1162 harmonic: 1730 Sorted by residual: dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual 93.00 17.59 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CA TYR f 52 " pdb=" C TYR f 52 " pdb=" N PRO f 53 " pdb=" CA PRO f 53 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual 93.00 157.95 -64.95 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 2889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 577 0.046 - 0.091: 146 0.091 - 0.137: 36 0.137 - 0.183: 5 0.183 - 0.229: 2 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA PRO b 29 " pdb=" N PRO b 29 " pdb=" C PRO b 29 " pdb=" CB PRO b 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C8 CLR b 201 " pdb=" C14 CLR b 201 " pdb=" C7 CLR b 201 " pdb=" C9 CLR b 201 " both_signs ideal model delta sigma weight residual False 2.69 2.50 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA PRO f 50 " pdb=" N PRO f 50 " pdb=" C PRO f 50 " pdb=" CB PRO f 50 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 763 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS e 104 " 0.097 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO e 105 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO e 105 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO e 105 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP b 28 " -0.075 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO b 29 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO b 29 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO b 29 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE d 24 " -0.057 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO d 25 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO d 25 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO d 25 " -0.045 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 164 2.70 - 3.25: 4515 3.25 - 3.80: 6823 3.80 - 4.35: 8310 4.35 - 4.90: 13932 Nonbonded interactions: 33744 Sorted by model distance: nonbonded pdb=" OD1 ASP e 78 " pdb=" N GLU e 79 " model vdw 2.154 3.120 nonbonded pdb=" N GLU d 30 " pdb=" OE1 GLU d 30 " model vdw 2.211 3.120 nonbonded pdb=" OD2 ASP g 35 " pdb=" OH TYR g 101 " model vdw 2.231 3.040 nonbonded pdb=" O LEU n 315 " pdb=" OG1 THR n 319 " model vdw 2.239 3.040 nonbonded pdb=" O PRO e 100 " pdb=" OG SER e 103 " model vdw 2.239 3.040 ... (remaining 33739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 28 through 46 or (resid 47 through 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 54)) selection = (chain 'b' and resid 28 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 47 or (resid 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 through 54 or (resid 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 67 or re \ sid 74 through 78 or (resid 79 through 80 and (name N or name CA or name C or na \ me O or name CB )) or resid 81 through 84 or (resid 85 through 86 and (name N or \ name CA or name C or name O or name CB )) or resid 87 through 98 or (resid 99 a \ nd (name N or name CA or name C or name O or name CB )) or resid 100 or (resid 1 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 102 through \ 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) or r \ esid 105 through 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 155)) selection = (chain 'f' and (resid 33 through 106 or (resid 107 through 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 155)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.130 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 4767 Z= 0.189 Angle : 0.918 16.333 6477 Z= 0.478 Chirality : 0.044 0.229 766 Planarity : 0.008 0.142 792 Dihedral : 18.669 79.500 1755 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.15 % Favored : 91.16 % Rotamer: Outliers : 1.38 % Allowed : 43.11 % Favored : 55.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.65 (0.34), residues: 577 helix: -0.04 (0.33), residues: 221 sheet: -0.85 (0.66), residues: 78 loop : -2.06 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 43 HIS 0.003 0.001 HIS f 81 PHE 0.013 0.001 PHE m 281 TYR 0.017 0.001 TYR a 42 ARG 0.007 0.000 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.30299 ( 221) hydrogen bonds : angle 7.38949 ( 636) SS BOND : bond 0.00409 ( 9) SS BOND : angle 1.67743 ( 18) covalent geometry : bond 0.00507 ( 4758) covalent geometry : angle 0.91537 ( 6459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: d 82 LYS cc_start: 0.4655 (tmtt) cc_final: 0.4009 (ptmt) REVERT: e 115 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7867 (mtp-110) REVERT: e 117 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7033 (ttt-90) REVERT: e 151 TRP cc_start: 0.7034 (t-100) cc_final: 0.6694 (t60) REVERT: f 33 GLN cc_start: 0.7243 (mm110) cc_final: 0.6933 (tp40) REVERT: f 100 PRO cc_start: 0.8064 (Cg_endo) cc_final: 0.7643 (Cg_exo) REVERT: f 137 ASP cc_start: 0.8077 (t70) cc_final: 0.7843 (t0) REVERT: f 153 LYS cc_start: 0.7444 (tppt) cc_final: 0.6766 (ttmm) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.1721 time to fit residues: 25.1075 Evaluate side-chains 99 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain f residue 126 ASP Chi-restraints excluded: chain g residue 39 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN g 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.189084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155499 restraints weight = 5961.583| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.01 r_work: 0.3590 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4767 Z= 0.186 Angle : 0.773 9.479 6477 Z= 0.392 Chirality : 0.045 0.222 766 Planarity : 0.006 0.078 792 Dihedral : 7.187 57.444 712 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.80 % Favored : 91.51 % Rotamer: Outliers : 8.07 % Allowed : 34.65 % Favored : 57.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.76 (0.35), residues: 577 helix: 1.35 (0.33), residues: 216 sheet: -0.60 (0.54), residues: 108 loop : -2.19 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.019 0.002 PHE m 281 TYR 0.014 0.002 TYR f 36 ARG 0.005 0.001 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.07446 ( 221) hydrogen bonds : angle 4.66000 ( 636) SS BOND : bond 0.00313 ( 9) SS BOND : angle 1.10641 ( 18) covalent geometry : bond 0.00430 ( 4758) covalent geometry : angle 0.77175 ( 6459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: b 46 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7931 (mt) REVERT: d 82 LYS cc_start: 0.4731 (tmtt) cc_final: 0.3782 (ptmt) REVERT: d 92 MET cc_start: 0.8411 (mmt) cc_final: 0.8146 (mmt) REVERT: e 33 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: e 89 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7415 (tm-30) REVERT: e 117 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7313 (ttt-90) REVERT: e 151 TRP cc_start: 0.7164 (t-100) cc_final: 0.6618 (t60) REVERT: f 33 GLN cc_start: 0.7416 (mm110) cc_final: 0.6956 (tp40) REVERT: f 56 GLU cc_start: 0.6065 (pm20) cc_final: 0.5769 (pm20) REVERT: f 153 LYS cc_start: 0.7240 (tppt) cc_final: 0.6626 (ttmm) outliers start: 41 outliers final: 26 residues processed: 121 average time/residue: 0.1567 time to fit residues: 24.2471 Evaluate side-chains 113 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.186888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155552 restraints weight = 5951.269| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.39 r_work: 0.3504 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4767 Z= 0.190 Angle : 0.749 7.972 6477 Z= 0.380 Chirality : 0.045 0.223 766 Planarity : 0.005 0.075 792 Dihedral : 6.762 55.042 705 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.63 % Favored : 91.68 % Rotamer: Outliers : 9.84 % Allowed : 32.48 % Favored : 57.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.57 (0.35), residues: 577 helix: 1.74 (0.33), residues: 216 sheet: -0.70 (0.54), residues: 108 loop : -2.22 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.017 0.002 PHE m 281 TYR 0.015 0.002 TYR f 36 ARG 0.003 0.001 ARG e 117 Details of bonding type rmsd hydrogen bonds : bond 0.07268 ( 221) hydrogen bonds : angle 4.45412 ( 636) SS BOND : bond 0.00306 ( 9) SS BOND : angle 1.16032 ( 18) covalent geometry : bond 0.00439 ( 4758) covalent geometry : angle 0.74767 ( 6459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 82 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6202 (t80) REVERT: e 89 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7737 (tm-30) REVERT: e 117 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7454 (ttt-90) REVERT: e 151 TRP cc_start: 0.7195 (t-100) cc_final: 0.6636 (t60) REVERT: f 33 GLN cc_start: 0.7402 (mm110) cc_final: 0.6927 (tp40) REVERT: f 56 GLU cc_start: 0.6030 (pm20) cc_final: 0.5828 (pm20) REVERT: f 153 LYS cc_start: 0.7374 (tppt) cc_final: 0.6823 (tttt) outliers start: 50 outliers final: 33 residues processed: 122 average time/residue: 0.1611 time to fit residues: 24.9989 Evaluate side-chains 113 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 83 SER Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 82 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.0000 chunk 7 optimal weight: 1.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 33 GLN n 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158673 restraints weight = 6002.903| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.19 r_work: 0.3614 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4767 Z= 0.134 Angle : 0.654 7.188 6477 Z= 0.333 Chirality : 0.042 0.162 766 Planarity : 0.005 0.071 792 Dihedral : 6.270 56.099 705 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.76 % Favored : 92.55 % Rotamer: Outliers : 9.06 % Allowed : 33.07 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.23 (0.36), residues: 577 helix: 2.24 (0.34), residues: 216 sheet: -0.44 (0.57), residues: 97 loop : -2.22 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 43 HIS 0.001 0.001 HIS g 29 PHE 0.011 0.001 PHE m 281 TYR 0.009 0.001 TYR e 99 ARG 0.003 0.000 ARG f 155 Details of bonding type rmsd hydrogen bonds : bond 0.05383 ( 221) hydrogen bonds : angle 4.01720 ( 636) SS BOND : bond 0.00295 ( 9) SS BOND : angle 1.15786 ( 18) covalent geometry : bond 0.00293 ( 4758) covalent geometry : angle 0.65213 ( 6459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.5056 (OUTLIER) cc_final: 0.4749 (mm) REVERT: b 40 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.5889 (t80) REVERT: b 46 LEU cc_start: 0.8430 (tp) cc_final: 0.8031 (mt) REVERT: d 82 LYS cc_start: 0.4639 (tptt) cc_final: 0.4077 (ptpp) REVERT: e 89 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7656 (tm-30) REVERT: e 117 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7354 (ttt-90) REVERT: e 150 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7637 (t80) REVERT: e 151 TRP cc_start: 0.7277 (t-100) cc_final: 0.6748 (t60) REVERT: f 56 GLU cc_start: 0.6166 (pm20) cc_final: 0.5908 (pm20) outliers start: 46 outliers final: 31 residues processed: 119 average time/residue: 0.1674 time to fit residues: 25.1057 Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 83 SER Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 150 TYR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Chi-restraints excluded: chain n residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.189898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158847 restraints weight = 6067.404| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.13 r_work: 0.3585 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4767 Z= 0.144 Angle : 0.677 9.797 6477 Z= 0.339 Chirality : 0.043 0.170 766 Planarity : 0.005 0.071 792 Dihedral : 6.301 52.574 705 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 8.46 % Allowed : 35.04 % Favored : 56.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.21 (0.36), residues: 577 helix: 2.31 (0.34), residues: 216 sheet: -0.46 (0.57), residues: 97 loop : -2.26 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.013 0.001 PHE m 281 TYR 0.015 0.001 TYR e 99 ARG 0.003 0.000 ARG f 155 Details of bonding type rmsd hydrogen bonds : bond 0.05734 ( 221) hydrogen bonds : angle 3.98928 ( 636) SS BOND : bond 0.00290 ( 9) SS BOND : angle 1.17245 ( 18) covalent geometry : bond 0.00324 ( 4758) covalent geometry : angle 0.67555 ( 6459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4783 (mm) REVERT: b 40 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.5706 (t80) REVERT: b 46 LEU cc_start: 0.8293 (tp) cc_final: 0.8061 (mt) REVERT: d 82 LYS cc_start: 0.4301 (tptt) cc_final: 0.3508 (ptpp) REVERT: e 117 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7353 (ttt-90) REVERT: e 151 TRP cc_start: 0.7221 (t-100) cc_final: 0.6682 (t60) REVERT: f 56 GLU cc_start: 0.5927 (pm20) cc_final: 0.5603 (pm20) outliers start: 43 outliers final: 37 residues processed: 118 average time/residue: 0.1719 time to fit residues: 25.5774 Evaluate side-chains 123 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 150 TYR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.188344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155031 restraints weight = 5904.486| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.28 r_work: 0.3556 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4767 Z= 0.168 Angle : 0.716 9.556 6477 Z= 0.359 Chirality : 0.044 0.187 766 Planarity : 0.005 0.074 792 Dihedral : 6.351 54.272 705 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.63 % Favored : 91.68 % Rotamer: Outliers : 10.43 % Allowed : 32.28 % Favored : 57.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.37 (0.35), residues: 577 helix: 2.24 (0.34), residues: 215 sheet: -0.81 (0.55), residues: 102 loop : -2.28 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.017 0.002 PHE m 281 TYR 0.013 0.001 TYR e 99 ARG 0.005 0.001 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.06409 ( 221) hydrogen bonds : angle 4.15759 ( 636) SS BOND : bond 0.00345 ( 9) SS BOND : angle 1.29316 ( 18) covalent geometry : bond 0.00385 ( 4758) covalent geometry : angle 0.71364 ( 6459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.5521 (t80) REVERT: b 46 LEU cc_start: 0.8396 (tp) cc_final: 0.8010 (tt) REVERT: e 117 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7353 (ttt-90) REVERT: e 151 TRP cc_start: 0.7222 (t-100) cc_final: 0.6649 (t60) REVERT: f 56 GLU cc_start: 0.5848 (pm20) cc_final: 0.5424 (pm20) REVERT: n 279 ASP cc_start: 0.4499 (OUTLIER) cc_final: 0.3932 (p0) REVERT: n 283 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.6191 (m) outliers start: 53 outliers final: 44 residues processed: 126 average time/residue: 0.1590 time to fit residues: 25.3502 Evaluate side-chains 132 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 83 SER Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 279 ASP Chi-restraints excluded: chain n residue 283 THR Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.189706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158699 restraints weight = 5923.362| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.05 r_work: 0.3575 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4767 Z= 0.150 Angle : 0.689 9.737 6477 Z= 0.344 Chirality : 0.043 0.176 766 Planarity : 0.005 0.073 792 Dihedral : 6.201 54.455 705 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.93 % Favored : 92.37 % Rotamer: Outliers : 10.83 % Allowed : 32.68 % Favored : 56.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.27 (0.36), residues: 577 helix: 2.34 (0.34), residues: 215 sheet: -0.71 (0.56), residues: 102 loop : -2.27 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.014 0.001 PHE m 281 TYR 0.013 0.001 TYR e 99 ARG 0.004 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 221) hydrogen bonds : angle 4.04330 ( 636) SS BOND : bond 0.00309 ( 9) SS BOND : angle 1.26478 ( 18) covalent geometry : bond 0.00342 ( 4758) covalent geometry : angle 0.68650 ( 6459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 89 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6592 (pp) REVERT: b 40 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.5734 (t80) REVERT: b 46 LEU cc_start: 0.8398 (tp) cc_final: 0.8017 (tt) REVERT: b 52 ARG cc_start: 0.6637 (tpp-160) cc_final: 0.6345 (tpp-160) REVERT: e 117 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7365 (ttt-90) REVERT: e 151 TRP cc_start: 0.7204 (t-100) cc_final: 0.6627 (t60) REVERT: f 56 GLU cc_start: 0.5885 (pm20) cc_final: 0.5470 (pm20) REVERT: n 279 ASP cc_start: 0.4497 (OUTLIER) cc_final: 0.4134 (p0) outliers start: 55 outliers final: 42 residues processed: 129 average time/residue: 0.1679 time to fit residues: 27.4093 Evaluate side-chains 131 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 40 PHE Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 279 ASP Chi-restraints excluded: chain n residue 301 LEU Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.0770 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161202 restraints weight = 6072.997| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.30 r_work: 0.3645 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4767 Z= 0.122 Angle : 0.642 8.799 6477 Z= 0.322 Chirality : 0.042 0.171 766 Planarity : 0.005 0.068 792 Dihedral : 5.825 54.188 705 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.59 % Favored : 92.72 % Rotamer: Outliers : 8.66 % Allowed : 34.65 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 0.04 (0.37), residues: 577 helix: 2.65 (0.34), residues: 215 sheet: -0.56 (0.57), residues: 102 loop : -2.14 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 151 HIS 0.002 0.001 HIS g 29 PHE 0.009 0.001 PHE m 281 TYR 0.014 0.001 TYR e 99 ARG 0.006 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 221) hydrogen bonds : angle 3.76175 ( 636) SS BOND : bond 0.00240 ( 9) SS BOND : angle 1.15854 ( 18) covalent geometry : bond 0.00271 ( 4758) covalent geometry : angle 0.63974 ( 6459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6543 (pp) REVERT: b 46 LEU cc_start: 0.8284 (tp) cc_final: 0.7925 (tt) REVERT: e 52 TYR cc_start: 0.7888 (t80) cc_final: 0.7579 (t80) REVERT: e 117 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7345 (ttt-90) REVERT: e 151 TRP cc_start: 0.7146 (t-100) cc_final: 0.6566 (t60) REVERT: f 56 GLU cc_start: 0.6035 (pm20) cc_final: 0.5601 (pm20) REVERT: g 61 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: g 109 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7984 (mm-30) REVERT: n 279 ASP cc_start: 0.4486 (m-30) cc_final: 0.4014 (p0) REVERT: n 283 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5871 (m) outliers start: 44 outliers final: 34 residues processed: 125 average time/residue: 0.1652 time to fit residues: 26.3640 Evaluate side-chains 121 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 283 THR Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.195359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161764 restraints weight = 5861.396| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.41 r_work: 0.3761 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4767 Z= 0.141 Angle : 0.688 9.759 6477 Z= 0.343 Chirality : 0.042 0.178 766 Planarity : 0.005 0.068 792 Dihedral : 6.069 57.364 705 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.93 % Favored : 92.37 % Rotamer: Outliers : 8.07 % Allowed : 36.02 % Favored : 55.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.06 (0.36), residues: 577 helix: 2.51 (0.34), residues: 215 sheet: -0.67 (0.56), residues: 102 loop : -2.12 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.013 0.001 PHE m 281 TYR 0.016 0.001 TYR e 99 ARG 0.007 0.001 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 221) hydrogen bonds : angle 3.86030 ( 636) SS BOND : bond 0.00287 ( 9) SS BOND : angle 1.25189 ( 18) covalent geometry : bond 0.00326 ( 4758) covalent geometry : angle 0.68544 ( 6459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6609 (pp) REVERT: b 46 LEU cc_start: 0.8292 (tp) cc_final: 0.8028 (tt) REVERT: e 52 TYR cc_start: 0.7818 (t80) cc_final: 0.7553 (t80) REVERT: e 117 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7409 (ttt-90) REVERT: e 151 TRP cc_start: 0.7103 (t-100) cc_final: 0.6699 (t60) REVERT: f 56 GLU cc_start: 0.6278 (pm20) cc_final: 0.5939 (pm20) REVERT: n 279 ASP cc_start: 0.4618 (m-30) cc_final: 0.4168 (p0) REVERT: n 283 THR cc_start: 0.6509 (OUTLIER) cc_final: 0.6228 (m) outliers start: 41 outliers final: 36 residues processed: 114 average time/residue: 0.1650 time to fit residues: 23.7388 Evaluate side-chains 120 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 283 THR Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN e 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.193594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.162970 restraints weight = 5835.903| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.08 r_work: 0.3726 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4767 Z= 0.154 Angle : 0.714 9.854 6477 Z= 0.357 Chirality : 0.043 0.182 766 Planarity : 0.005 0.070 792 Dihedral : 6.271 57.740 705 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.11 % Favored : 92.20 % Rotamer: Outliers : 8.46 % Allowed : 35.83 % Favored : 55.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.17 (0.36), residues: 577 helix: 2.39 (0.34), residues: 215 sheet: -0.76 (0.55), residues: 102 loop : -2.13 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.015 0.002 PHE m 281 TYR 0.016 0.001 TYR e 99 ARG 0.007 0.001 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 221) hydrogen bonds : angle 3.95044 ( 636) SS BOND : bond 0.00307 ( 9) SS BOND : angle 1.23666 ( 18) covalent geometry : bond 0.00355 ( 4758) covalent geometry : angle 0.71207 ( 6459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 LEU cc_start: 0.8265 (tp) cc_final: 0.8044 (tt) REVERT: e 52 TYR cc_start: 0.7756 (t80) cc_final: 0.7462 (t80) REVERT: e 117 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7416 (ttt-90) REVERT: e 151 TRP cc_start: 0.7130 (t-100) cc_final: 0.6738 (t60) REVERT: f 56 GLU cc_start: 0.6101 (pm20) cc_final: 0.5852 (pm20) REVERT: n 279 ASP cc_start: 0.4600 (OUTLIER) cc_final: 0.4275 (p0) REVERT: n 283 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6495 (m) outliers start: 43 outliers final: 40 residues processed: 112 average time/residue: 0.1667 time to fit residues: 23.5465 Evaluate side-chains 122 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 255 HIS Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain m residue 287 LEU Chi-restraints excluded: chain n residue 279 ASP Chi-restraints excluded: chain n residue 283 THR Chi-restraints excluded: chain n residue 304 SER Chi-restraints excluded: chain n residue 313 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN ** g 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.192968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162416 restraints weight = 5861.782| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.07 r_work: 0.3718 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4767 Z= 0.157 Angle : 0.709 10.005 6477 Z= 0.356 Chirality : 0.043 0.182 766 Planarity : 0.005 0.073 792 Dihedral : 6.194 54.956 705 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.28 % Favored : 92.03 % Rotamer: Outliers : 8.66 % Allowed : 35.63 % Favored : 55.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -0.22 (0.36), residues: 577 helix: 2.34 (0.34), residues: 215 sheet: -0.78 (0.55), residues: 102 loop : -2.14 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.015 0.002 PHE m 281 TYR 0.015 0.001 TYR e 99 ARG 0.007 0.001 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.05803 ( 221) hydrogen bonds : angle 4.00180 ( 636) SS BOND : bond 0.00320 ( 9) SS BOND : angle 1.27635 ( 18) covalent geometry : bond 0.00364 ( 4758) covalent geometry : angle 0.70690 ( 6459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.85 seconds wall clock time: 46 minutes 20.43 seconds (2780.43 seconds total)