Starting phenix.real_space_refine on Wed Sep 17 04:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8za6_39874/09_2025/8za6_39874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8za6_39874/09_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_39874/09_2025/8za6_39874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8za6_39874/09_2025/8za6_39874.map" model { file = "/net/cci-nas-00/data/ceres_data/8za6_39874/09_2025/8za6_39874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8za6_39874/09_2025/8za6_39874.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 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: 1.53, per 1000 atoms: 0.33 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: 0.42 Conformation dependent library (CDL) restraints added in 137.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.19 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: 0.70 Time building geometry restraints manager: 0.59 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG e 117 TYR 0.017 0.001 TYR a 42 PHE 0.013 0.001 PHE m 281 TRP 0.005 0.001 TRP d 43 HIS 0.003 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 4758) covalent geometry : angle 0.91537 ( 6459) SS BOND : bond 0.00409 ( 9) SS BOND : angle 1.67743 ( 18) hydrogen bonds : bond 0.30299 ( 221) hydrogen bonds : angle 7.38949 ( 636) *********************** 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 : 0.195 Fit side-chains revert: symmetry clash REVERT: d 82 LYS cc_start: 0.4655 (tmtt) cc_final: 0.4008 (ptmt) REVERT: e 115 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7866 (mtp-110) REVERT: e 117 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7032 (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: 0.6932 (tp40) REVERT: f 100 PRO cc_start: 0.8064 (Cg_endo) cc_final: 0.7642 (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) REVERT: g 88 LYS cc_start: 0.4877 (tptt) cc_final: 0.4610 (tptp) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.0845 time to fit residues: 12.2927 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 : 0.112 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.192679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159716 restraints weight = 5942.927| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.77 r_work: 0.3638 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4767 Z= 0.159 Angle : 0.731 9.418 6477 Z= 0.372 Chirality : 0.044 0.163 766 Planarity : 0.006 0.078 792 Dihedral : 7.061 56.771 712 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.28 % Favored : 92.03 % Rotamer: Outliers : 7.68 % Allowed : 34.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.35), residues: 577 helix: 1.56 (0.33), residues: 216 sheet: -0.05 (0.58), residues: 97 loop : -2.25 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 117 TYR 0.012 0.001 TYR e 99 PHE 0.016 0.001 PHE m 281 TRP 0.008 0.001 TRP d 43 HIS 0.002 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4758) covalent geometry : angle 0.73066 ( 6459) SS BOND : bond 0.00259 ( 9) SS BOND : angle 0.95559 ( 18) hydrogen bonds : bond 0.06848 ( 221) hydrogen bonds : angle 4.52299 ( 636) *********************** 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: 39 poor density : 95 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: d 82 LYS cc_start: 0.4481 (tmtt) cc_final: 0.3738 (ptmt) REVERT: d 92 MET cc_start: 0.8273 (mmt) cc_final: 0.8029 (mmt) REVERT: e 117 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7340 (ttt-90) REVERT: e 151 TRP cc_start: 0.7307 (t-100) cc_final: 0.6684 (t60) REVERT: f 33 GLN cc_start: 0.7327 (mm110) cc_final: 0.6911 (tp40) REVERT: f 56 GLU cc_start: 0.6018 (pm20) cc_final: 0.5769 (pm20) REVERT: f 153 LYS cc_start: 0.7300 (tppt) cc_final: 0.6663 (ttmm) REVERT: g 88 LYS cc_start: 0.4587 (tptt) cc_final: 0.4334 (tppt) REVERT: m 262 MET cc_start: 0.8051 (tpp) cc_final: 0.7702 (tpp) outliers start: 39 outliers final: 24 residues processed: 122 average time/residue: 0.0732 time to fit residues: 11.3903 Evaluate side-chains 108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 84 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 57 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 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.190999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158875 restraints weight = 6057.652| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.01 r_work: 0.3590 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2540 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= 0.152 Angle : 0.694 7.530 6477 Z= 0.351 Chirality : 0.044 0.168 766 Planarity : 0.005 0.073 792 Dihedral : 6.528 53.919 705 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.93 % Favored : 92.37 % Rotamer: Outliers : 8.66 % Allowed : 34.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.35), residues: 577 helix: 2.03 (0.33), residues: 216 sheet: -0.44 (0.56), residues: 102 loop : -2.23 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.015 0.001 TYR e 99 PHE 0.014 0.001 PHE m 281 TRP 0.006 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4758) covalent geometry : angle 0.69305 ( 6459) SS BOND : bond 0.00299 ( 9) SS BOND : angle 1.03211 ( 18) hydrogen bonds : bond 0.06382 ( 221) hydrogen bonds : angle 4.19004 ( 636) *********************** 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 127 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: a 46 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4440 (mm) REVERT: b 40 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.5562 (t80) REVERT: d 82 LYS cc_start: 0.4766 (tmtt) cc_final: 0.3771 (ptmt) REVERT: e 117 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7418 (ttt-90) REVERT: e 151 TRP cc_start: 0.7346 (t-100) cc_final: 0.6678 (t60) REVERT: f 33 GLN cc_start: 0.7412 (mm110) cc_final: 0.7001 (tp40) REVERT: f 153 LYS cc_start: 0.7390 (tppt) cc_final: 0.6825 (tttp) outliers start: 44 outliers final: 23 residues processed: 114 average time/residue: 0.0741 time to fit residues: 10.8306 Evaluate side-chains 104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 150 TYR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158749 restraints weight = 6006.475| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.07 r_work: 0.3607 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2894 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= 0.141 Angle : 0.674 7.732 6477 Z= 0.338 Chirality : 0.043 0.168 766 Planarity : 0.005 0.070 792 Dihedral : 6.305 54.198 705 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.59 % Favored : 92.72 % Rotamer: Outliers : 7.87 % Allowed : 35.24 % Favored : 56.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.36), residues: 577 helix: 2.27 (0.33), residues: 216 sheet: -0.55 (0.57), residues: 96 loop : -2.16 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 155 TYR 0.013 0.001 TYR f 149 PHE 0.013 0.001 PHE m 281 TRP 0.007 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4758) covalent geometry : angle 0.67310 ( 6459) SS BOND : bond 0.00416 ( 9) SS BOND : angle 1.04289 ( 18) hydrogen bonds : bond 0.05617 ( 221) hydrogen bonds : angle 4.00021 ( 636) *********************** 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 129 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: a 46 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4610 (mm) REVERT: b 46 LEU cc_start: 0.8297 (tp) cc_final: 0.7926 (mp) REVERT: e 117 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7466 (ttt-90) REVERT: e 151 TRP cc_start: 0.7271 (t-100) cc_final: 0.6737 (t60) REVERT: f 33 GLN cc_start: 0.7416 (mm110) cc_final: 0.7043 (tp40) REVERT: f 56 GLU cc_start: 0.5983 (pm20) cc_final: 0.5663 (pm20) REVERT: g 109 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7970 (mm-30) outliers start: 40 outliers final: 27 residues processed: 119 average time/residue: 0.0780 time to fit residues: 11.7998 Evaluate side-chains 110 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 a residue 46 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 48 VAL 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 84 LEU 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 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 108 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN ** n 290 ASN ** 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 = 0.4216 r_free = 0.4216 target = 0.190489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157684 restraints weight = 6040.501| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.14 r_work: 0.3595 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3084 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= 0.140 Angle : 0.678 9.893 6477 Z= 0.340 Chirality : 0.043 0.167 766 Planarity : 0.005 0.070 792 Dihedral : 6.275 54.462 705 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.24 % Favored : 93.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.35), residues: 577 helix: 2.41 (0.33), residues: 216 sheet: -0.35 (0.58), residues: 91 loop : -2.27 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 52 TYR 0.014 0.001 TYR e 99 PHE 0.014 0.001 PHE m 281 TRP 0.008 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4758) covalent geometry : angle 0.67587 ( 6459) SS BOND : bond 0.00276 ( 9) SS BOND : angle 1.13588 ( 18) hydrogen bonds : bond 0.05503 ( 221) hydrogen bonds : angle 3.90340 ( 636) *********************** 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 130 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.5641 (t80) REVERT: b 46 LEU cc_start: 0.8289 (tp) cc_final: 0.7715 (tt) REVERT: d 82 LYS cc_start: 0.4007 (tptt) cc_final: 0.3391 (ptpt) REVERT: e 33 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: e 117 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7380 (ttt-90) REVERT: e 150 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7579 (t80) REVERT: e 151 TRP cc_start: 0.7235 (t-100) cc_final: 0.6699 (t60) REVERT: f 33 GLN cc_start: 0.7447 (mm110) cc_final: 0.7081 (tp40) REVERT: f 56 GLU cc_start: 0.5879 (pm20) cc_final: 0.5375 (pm20) REVERT: f 153 LYS cc_start: 0.7084 (tppt) cc_final: 0.6443 (tttp) REVERT: g 109 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7908 (mm-30) outliers start: 44 outliers final: 36 residues processed: 116 average time/residue: 0.0830 time to fit residues: 12.1368 Evaluate side-chains 122 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 44 VAL 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 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 122 VAL Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 150 TYR 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 98 CYS 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 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 Chi-restraints excluded: chain n residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** n 290 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.186321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151864 restraints weight = 6116.958| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.28 r_work: 0.3512 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4767 Z= 0.200 Angle : 0.750 10.363 6477 Z= 0.379 Chirality : 0.046 0.244 766 Planarity : 0.006 0.075 792 Dihedral : 6.540 53.414 705 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.63 % Favored : 91.68 % Rotamer: Outliers : 9.06 % Allowed : 33.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.35), residues: 577 helix: 2.03 (0.34), residues: 216 sheet: -0.79 (0.57), residues: 96 loop : -2.36 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 52 TYR 0.015 0.002 TYR f 36 PHE 0.021 0.002 PHE m 281 TRP 0.011 0.001 TRP d 43 HIS 0.004 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4758) covalent geometry : angle 0.74760 ( 6459) SS BOND : bond 0.00359 ( 9) SS BOND : angle 1.36512 ( 18) hydrogen bonds : bond 0.07049 ( 221) hydrogen bonds : angle 4.28686 ( 636) *********************** 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 130 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6184 (t80) REVERT: d 82 LYS cc_start: 0.4041 (tptt) cc_final: 0.3373 (ptpp) REVERT: e 52 TYR cc_start: 0.7789 (t80) cc_final: 0.7288 (t80) REVERT: e 117 ARG cc_start: 0.8385 (ttm110) cc_final: 0.7390 (ttt-90) REVERT: e 151 TRP cc_start: 0.7246 (t-100) cc_final: 0.6660 (t60) REVERT: f 33 GLN cc_start: 0.7484 (mm110) cc_final: 0.7066 (tp40) REVERT: f 56 GLU cc_start: 0.5847 (pm20) cc_final: 0.5598 (pm20) REVERT: g 109 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7922 (mm-30) REVERT: n 279 ASP cc_start: 0.4672 (OUTLIER) cc_final: 0.3909 (p0) REVERT: n 283 THR cc_start: 0.6587 (OUTLIER) cc_final: 0.6378 (m) outliers start: 46 outliers final: 35 residues processed: 117 average time/residue: 0.0821 time to fit residues: 11.9929 Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 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 84 LEU Chi-restraints excluded: chain e residue 145 LEU 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 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 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 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** n 290 ASN ** 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 = 0.4200 r_free = 0.4200 target = 0.188587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155046 restraints weight = 6011.525| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.26 r_work: 0.3568 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3202 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= 0.153 Angle : 0.687 8.923 6477 Z= 0.347 Chirality : 0.043 0.168 766 Planarity : 0.005 0.072 792 Dihedral : 6.212 54.342 705 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.11 % Favored : 92.20 % Rotamer: Outliers : 8.86 % Allowed : 34.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.35), residues: 577 helix: 2.27 (0.34), residues: 215 sheet: -0.74 (0.57), residues: 96 loop : -2.36 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 52 TYR 0.016 0.001 TYR e 99 PHE 0.015 0.001 PHE m 281 TRP 0.009 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4758) covalent geometry : angle 0.68504 ( 6459) SS BOND : bond 0.00300 ( 9) SS BOND : angle 1.27819 ( 18) hydrogen bonds : bond 0.05916 ( 221) hydrogen bonds : angle 4.06975 ( 636) *********************** 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 131 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6576 (pp) REVERT: b 40 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.5787 (t80) REVERT: b 46 LEU cc_start: 0.8389 (tp) cc_final: 0.7981 (tt) REVERT: b 52 ARG cc_start: 0.6713 (tpp-160) cc_final: 0.6407 (tpp-160) REVERT: d 92 MET cc_start: 0.7862 (mmt) cc_final: 0.7622 (mmt) REVERT: e 117 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7351 (ttt-90) REVERT: e 151 TRP cc_start: 0.7211 (t-100) cc_final: 0.6628 (t60) REVERT: f 56 GLU cc_start: 0.5958 (pm20) cc_final: 0.5705 (pm20) REVERT: g 109 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7875 (mm-30) REVERT: n 279 ASP cc_start: 0.4601 (m-30) cc_final: 0.4073 (p0) outliers start: 45 outliers final: 36 residues processed: 118 average time/residue: 0.0837 time to fit residues: 12.3520 Evaluate side-chains 122 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 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 124 CYS 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 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 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 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 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 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 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 33 GLN n 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156834 restraints weight = 6119.425| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.21 r_work: 0.3606 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3448 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= 0.131 Angle : 0.666 8.132 6477 Z= 0.335 Chirality : 0.043 0.174 766 Planarity : 0.005 0.069 792 Dihedral : 5.898 54.592 705 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.11 % Favored : 92.20 % Rotamer: Outliers : 8.86 % Allowed : 34.84 % Favored : 56.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.36), residues: 577 helix: 2.50 (0.34), residues: 216 sheet: -0.68 (0.57), residues: 96 loop : -2.30 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 52 TYR 0.014 0.001 TYR e 99 PHE 0.011 0.001 PHE m 281 TRP 0.007 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4758) covalent geometry : angle 0.66361 ( 6459) SS BOND : bond 0.00300 ( 9) SS BOND : angle 1.16910 ( 18) hydrogen bonds : bond 0.05078 ( 221) hydrogen bonds : angle 3.85066 ( 636) *********************** 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 131 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6566 (pp) REVERT: b 40 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.5832 (t80) REVERT: b 46 LEU cc_start: 0.8278 (tp) cc_final: 0.7734 (tt) REVERT: e 52 TYR cc_start: 0.7859 (t80) cc_final: 0.7524 (t80) REVERT: e 85 LYS cc_start: 0.8607 (mptt) cc_final: 0.8390 (mppt) REVERT: e 117 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7307 (ttt-90) REVERT: e 151 TRP cc_start: 0.7172 (t-100) cc_final: 0.6605 (t60) REVERT: f 56 GLU cc_start: 0.5983 (pm20) cc_final: 0.5701 (pm20) REVERT: g 109 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7859 (mm-30) REVERT: n 279 ASP cc_start: 0.4490 (m-30) cc_final: 0.4274 (p0) REVERT: n 283 THR cc_start: 0.6180 (OUTLIER) cc_final: 0.5967 (m) outliers start: 45 outliers final: 35 residues processed: 121 average time/residue: 0.0819 time to fit residues: 12.4855 Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 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 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 57 ILE Chi-restraints excluded: chain f residue 66 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 145 LEU 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 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 301 LEU Chi-restraints excluded: chain n residue 304 SER 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 24 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.193577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162728 restraints weight = 5830.367| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.04 r_work: 0.3721 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3409 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= 0.155 Angle : 0.706 11.080 6477 Z= 0.355 Chirality : 0.044 0.180 766 Planarity : 0.005 0.071 792 Dihedral : 6.141 56.648 705 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.45 % Favored : 91.85 % Rotamer: Outliers : 8.07 % Allowed : 35.83 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.36), residues: 577 helix: 2.41 (0.34), residues: 215 sheet: -0.68 (0.57), residues: 96 loop : -2.30 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 52 TYR 0.015 0.001 TYR e 99 PHE 0.015 0.001 PHE m 281 TRP 0.008 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4758) covalent geometry : angle 0.70397 ( 6459) SS BOND : bond 0.00314 ( 9) SS BOND : angle 1.24885 ( 18) hydrogen bonds : bond 0.05710 ( 221) hydrogen bonds : angle 3.97660 ( 636) *********************** 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 : 0.200 Fit side-chains revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.5467 (t80) REVERT: b 46 LEU cc_start: 0.8411 (tp) cc_final: 0.7946 (tt) REVERT: e 52 TYR cc_start: 0.7747 (t80) cc_final: 0.7437 (t80) REVERT: e 117 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7502 (ttt-90) REVERT: e 151 TRP cc_start: 0.7139 (t-100) cc_final: 0.6721 (t60) REVERT: f 56 GLU cc_start: 0.6225 (pm20) cc_final: 0.6014 (pm20) REVERT: g 73 ASN cc_start: 0.8849 (t0) cc_final: 0.8644 (t0) REVERT: n 283 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6539 (m) outliers start: 41 outliers final: 36 residues processed: 113 average time/residue: 0.0856 time to fit residues: 12.1131 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 : 0.185 ------------------------------------------------------------------------------- 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 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 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 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 57 ILE Chi-restraints excluded: chain f residue 66 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 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 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 ** 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 = 0.4224 r_free = 0.4224 target = 0.190669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157382 restraints weight = 5982.798| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.25 r_work: 0.3580 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3421 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= 0.152 Angle : 0.700 10.887 6477 Z= 0.351 Chirality : 0.043 0.184 766 Planarity : 0.005 0.072 792 Dihedral : 6.169 56.601 705 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.93 % Favored : 92.37 % Rotamer: Outliers : 8.07 % Allowed : 35.83 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.36), residues: 577 helix: 2.37 (0.34), residues: 216 sheet: -0.68 (0.57), residues: 96 loop : -2.29 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 52 TYR 0.015 0.001 TYR e 99 PHE 0.014 0.001 PHE m 281 TRP 0.008 0.001 TRP d 43 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4758) covalent geometry : angle 0.69825 ( 6459) SS BOND : bond 0.00317 ( 9) SS BOND : angle 1.21728 ( 18) hydrogen bonds : bond 0.05717 ( 221) hydrogen bonds : angle 3.97544 ( 636) ********************** 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: 41 poor density : 83 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.5594 (t80) REVERT: b 46 LEU cc_start: 0.8272 (tp) cc_final: 0.7890 (tt) REVERT: e 52 TYR cc_start: 0.7794 (t80) cc_final: 0.7447 (t80) REVERT: e 117 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7423 (ttt-90) REVERT: e 151 TRP cc_start: 0.7184 (t-100) cc_final: 0.6605 (t60) REVERT: f 56 GLU cc_start: 0.5921 (pm20) cc_final: 0.5577 (pm20) REVERT: n 283 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6324 (m) outliers start: 41 outliers final: 35 residues processed: 112 average time/residue: 0.0800 time to fit residues: 11.3422 Evaluate side-chains 119 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 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 124 CYS 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 57 ILE Chi-restraints excluded: chain f residue 66 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 146 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.195088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164373 restraints weight = 5880.857| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.06 r_work: 0.3749 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3545 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= 0.138 Angle : 0.685 10.441 6477 Z= 0.345 Chirality : 0.043 0.179 766 Planarity : 0.005 0.070 792 Dihedral : 6.097 57.486 705 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.59 % Favored : 92.89 % Rotamer: Outliers : 7.48 % Allowed : 36.42 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.36), residues: 577 helix: 2.48 (0.34), residues: 216 sheet: -0.62 (0.57), residues: 96 loop : -2.27 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 52 TYR 0.014 0.001 TYR e 99 PHE 0.012 0.001 PHE m 281 TRP 0.006 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4758) covalent geometry : angle 0.68301 ( 6459) SS BOND : bond 0.00303 ( 9) SS BOND : angle 1.25433 ( 18) hydrogen bonds : bond 0.05210 ( 221) hydrogen bonds : angle 3.85663 ( 636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1358.63 seconds wall clock time: 24 minutes 3.40 seconds (1443.40 seconds total)