Starting phenix.real_space_refine on Sat Apr 6 11:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/04_2024/7jz3_22529_neut.pdb" } resolution = 2.56 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.212 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 9 5.16 5 C 5097 2.51 5 N 1374 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8142 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Time building chain proxies: 4.62, per 1000 atoms: 0.57 Number of scatterers: 8142 At special positions: 0 Unit cell: (93.96, 92.88, 71.28, 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 9 16.00 O 1662 8.00 N 1374 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 6.4% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 5 current: chain 'B' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL B 75 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 59 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 73 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 61 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER B 71 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 91 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN B 93 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 126 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG B 217 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 244 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B 254 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 245 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP B 252 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 255 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 283 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 281 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 279 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY B 282 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 293 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 4 through 5 current: chain 'C' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL C 75 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 59 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR C 73 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 61 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 71 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 91 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 93 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN C 126 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG C 217 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 244 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C 254 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 245 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP C 252 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 255 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 283 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 281 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 279 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 282 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP C 293 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 5 current: chain 'A' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL A 75 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 59 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 73 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 61 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 71 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 91 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 93 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 126 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG A 217 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 244 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 254 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 245 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 252 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 255 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 283 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 281 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 279 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 265 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY A 282 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 293 " --> pdb=" O GLY A 282 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1089 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: 2.44 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2154 1.33 - 1.45: 1915 1.45 - 1.57: 4232 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8319 Sorted by residual: bond pdb=" CA ASN C 133 " pdb=" CB ASN C 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.37e+00 bond pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.26e+00 bond pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.55e-02 4.16e+03 6.21e+00 bond pdb=" N ASN C 133 " pdb=" CA ASN C 133 " ideal model delta sigma weight residual 1.455 1.427 0.028 1.22e-02 6.72e+03 5.39e+00 bond pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta sigma weight residual 1.455 1.428 0.028 1.22e-02 6.72e+03 5.11e+00 ... (remaining 8314 not shown) Histogram of bond angle deviations from ideal: 101.02 - 107.62: 151 107.62 - 114.22: 4230 114.22 - 120.82: 3613 120.82 - 127.42: 3238 127.42 - 134.02: 33 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N VAL B 29 " pdb=" CA VAL B 29 " pdb=" C VAL B 29 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N VAL C 29 " pdb=" CA VAL C 29 " pdb=" C VAL C 29 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" N GLY C 138 " pdb=" CA GLY C 138 " pdb=" C GLY C 138 " ideal model delta sigma weight residual 115.32 119.34 -4.02 1.38e+00 5.25e-01 8.49e+00 angle pdb=" N GLY B 138 " pdb=" CA GLY B 138 " pdb=" C GLY B 138 " ideal model delta sigma weight residual 115.32 119.33 -4.01 1.38e+00 5.25e-01 8.43e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4233 16.34 - 32.69: 365 32.69 - 49.03: 88 49.03 - 65.37: 15 65.37 - 81.71: 6 Dihedral angle restraints: 4707 sinusoidal: 1791 harmonic: 2916 Sorted by residual: dihedral pdb=" CA GLN A 237 " pdb=" CB GLN A 237 " pdb=" CG GLN A 237 " pdb=" CD GLN A 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.89 50.89 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " pdb=" CD GLN B 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.88 50.88 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN C 237 " pdb=" CB GLN C 237 " pdb=" CG GLN C 237 " pdb=" CD GLN C 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.86 50.86 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 4704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 722 0.037 - 0.073: 279 0.073 - 0.110: 91 0.110 - 0.147: 30 0.147 - 0.183: 6 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PHE C 136 " pdb=" N PHE C 136 " pdb=" C PHE C 136 " pdb=" CB PHE C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE B 136 " pdb=" N PHE B 136 " pdb=" C PHE B 136 " pdb=" CB PHE B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PHE A 136 " pdb=" N PHE A 136 " pdb=" C PHE A 136 " pdb=" CB PHE A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1125 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 84 " -0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CG ASP A 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 84 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" CG ASP C 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP C 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 84 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" CG ASP B 84 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP B 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 7936 3.29 - 3.82: 13672 3.82 - 4.36: 17117 4.36 - 4.90: 30181 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" NE2 GLN B 237 " pdb=" OG1 THR B 239 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN C 237 " pdb=" OG1 THR C 239 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN A 237 " pdb=" OG1 THR A 239 " model vdw 2.211 2.520 nonbonded pdb=" OD2 ASP A 89 " pdb=" ND2 ASN A 93 " model vdw 2.288 2.520 nonbonded pdb=" OD2 ASP B 89 " pdb=" ND2 ASN B 93 " model vdw 2.289 2.520 ... (remaining 69739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.390 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8319 Z= 0.213 Angle : 0.623 6.968 11265 Z= 0.384 Chirality : 0.046 0.183 1128 Planarity : 0.003 0.038 1530 Dihedral : 13.643 81.714 2913 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.09 % Allowed : 7.27 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1032 helix: -2.59 (0.66), residues: 42 sheet: -0.80 (0.20), residues: 561 loop : -2.78 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 56 HIS 0.002 0.001 HIS C 21 PHE 0.011 0.002 PHE B 269 TYR 0.012 0.001 TYR B 58 ARG 0.001 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5712 (mttm) cc_final: 0.5058 (mptt) REVERT: B 291 ASP cc_start: 0.5276 (m-30) cc_final: 0.4920 (t0) REVERT: C 281 LYS cc_start: 0.5715 (mttm) cc_final: 0.5460 (mttm) REVERT: C 310 MET cc_start: 0.7723 (tpt) cc_final: 0.7399 (tpt) REVERT: A 281 LYS cc_start: 0.5722 (mttm) cc_final: 0.5054 (mptt) REVERT: A 291 ASP cc_start: 0.5277 (m-30) cc_final: 0.4989 (t0) REVERT: A 319 ASN cc_start: 0.5859 (t0) cc_final: 0.5251 (t0) outliers start: 9 outliers final: 5 residues processed: 203 average time/residue: 0.9041 time to fit residues: 197.7861 Evaluate side-chains 156 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 21 HIS B 45 GLN B 61 GLN B 83 GLN B 144 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 9 ASN C 21 HIS C 45 GLN C 61 GLN C 69 ASN C 144 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN A 21 HIS A 45 GLN A 61 GLN A 69 ASN A 144 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8319 Z= 0.433 Angle : 0.852 11.769 11265 Z= 0.457 Chirality : 0.052 0.154 1128 Planarity : 0.005 0.048 1530 Dihedral : 6.091 52.070 1171 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.70 % Allowed : 19.03 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1032 helix: -3.08 (0.40), residues: 60 sheet: -0.59 (0.21), residues: 543 loop : -3.07 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 252 HIS 0.002 0.001 HIS A 21 PHE 0.037 0.003 PHE C 40 TYR 0.027 0.003 TYR C 313 ARG 0.007 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: B 281 LYS cc_start: 0.5740 (mttm) cc_final: 0.5192 (mttp) REVERT: C 27 LYS cc_start: 0.7232 (mptt) cc_final: 0.6605 (mptm) REVERT: C 219 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.4556 (mp0) REVERT: C 281 LYS cc_start: 0.5944 (mttm) cc_final: 0.5383 (mttp) REVERT: C 294 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6904 (mm) REVERT: A 281 LYS cc_start: 0.6118 (mttm) cc_final: 0.5291 (mptt) outliers start: 47 outliers final: 22 residues processed: 202 average time/residue: 0.9366 time to fit residues: 204.2426 Evaluate side-chains 184 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 304 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 144 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8319 Z= 0.226 Angle : 0.681 9.523 11265 Z= 0.364 Chirality : 0.047 0.159 1128 Planarity : 0.004 0.051 1530 Dihedral : 5.445 50.285 1169 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.06 % Allowed : 24.00 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1032 helix: -2.05 (0.64), residues: 60 sheet: -0.45 (0.21), residues: 552 loop : -2.76 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.001 0.001 HIS B 21 PHE 0.022 0.002 PHE C 40 TYR 0.020 0.002 TYR C 98 ARG 0.005 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5740 (mttm) cc_final: 0.5243 (mttp) REVERT: B 319 ASN cc_start: 0.6316 (t0) cc_final: 0.5940 (t0) REVERT: C 27 LYS cc_start: 0.7179 (mptt) cc_final: 0.6663 (mmtp) REVERT: C 219 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.4650 (mp0) REVERT: C 281 LYS cc_start: 0.5958 (mttm) cc_final: 0.5398 (mttp) REVERT: C 294 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6567 (mm) REVERT: C 345 GLN cc_start: 0.7234 (pt0) cc_final: 0.6909 (pt0) REVERT: A 122 GLN cc_start: 0.4693 (OUTLIER) cc_final: 0.2775 (tm-30) REVERT: A 281 LYS cc_start: 0.6119 (mttm) cc_final: 0.5562 (mttp) outliers start: 50 outliers final: 32 residues processed: 205 average time/residue: 0.9097 time to fit residues: 201.9637 Evaluate side-chains 200 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8319 Z= 0.349 Angle : 0.772 9.604 11265 Z= 0.414 Chirality : 0.050 0.218 1128 Planarity : 0.004 0.056 1530 Dihedral : 5.857 56.341 1168 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 7.64 % Allowed : 24.00 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.24), residues: 1032 helix: -2.07 (0.69), residues: 42 sheet: -0.38 (0.21), residues: 543 loop : -2.80 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 252 HIS 0.002 0.001 HIS A 21 PHE 0.022 0.003 PHE C 40 TYR 0.021 0.003 TYR C 98 ARG 0.005 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 252 TRP cc_start: 0.6501 (OUTLIER) cc_final: 0.5287 (m-90) REVERT: B 281 LYS cc_start: 0.5874 (mttm) cc_final: 0.5307 (mttp) REVERT: C 27 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6900 (mptt) REVERT: C 219 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.4518 (mp0) REVERT: C 281 LYS cc_start: 0.6087 (mttm) cc_final: 0.5356 (mttt) REVERT: C 294 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6630 (mm) REVERT: A 122 GLN cc_start: 0.4773 (OUTLIER) cc_final: 0.4497 (mt0) REVERT: A 281 LYS cc_start: 0.6223 (mttm) cc_final: 0.5699 (mttp) outliers start: 63 outliers final: 40 residues processed: 205 average time/residue: 0.8479 time to fit residues: 188.8032 Evaluate side-chains 209 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 322 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 8319 Z= 0.508 Angle : 0.917 10.432 11265 Z= 0.493 Chirality : 0.054 0.263 1128 Planarity : 0.005 0.057 1530 Dihedral : 6.537 59.850 1168 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 9.82 % Allowed : 24.97 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.24), residues: 1032 helix: -2.68 (0.60), residues: 42 sheet: -0.57 (0.22), residues: 528 loop : -2.95 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.024 0.003 PHE C 40 TYR 0.027 0.003 TYR A 221 ARG 0.007 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 170 time to evaluate : 0.958 Fit side-chains REVERT: B 252 TRP cc_start: 0.6664 (OUTLIER) cc_final: 0.5390 (m-90) REVERT: B 281 LYS cc_start: 0.5885 (mttm) cc_final: 0.5153 (mptt) REVERT: C 27 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7046 (mptt) REVERT: C 170 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5871 (ptp-170) REVERT: C 219 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.4601 (mp0) REVERT: C 281 LYS cc_start: 0.6052 (mttm) cc_final: 0.5505 (mttp) REVERT: C 294 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6617 (mm) REVERT: A 122 GLN cc_start: 0.4877 (OUTLIER) cc_final: 0.4566 (mt0) REVERT: A 252 TRP cc_start: 0.6777 (OUTLIER) cc_final: 0.5425 (m-90) REVERT: A 281 LYS cc_start: 0.6275 (mttm) cc_final: 0.5703 (mttp) outliers start: 81 outliers final: 44 residues processed: 219 average time/residue: 0.8829 time to fit residues: 209.3658 Evaluate side-chains 213 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 162 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 83 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8319 Z= 0.264 Angle : 0.734 9.672 11265 Z= 0.388 Chirality : 0.048 0.171 1128 Planarity : 0.004 0.057 1530 Dihedral : 5.778 54.851 1168 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 7.64 % Allowed : 28.36 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.25), residues: 1032 helix: -1.83 (0.73), residues: 42 sheet: -0.45 (0.22), residues: 543 loop : -2.72 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.019 0.002 PHE C 40 TYR 0.026 0.002 TYR C 98 ARG 0.006 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 174 time to evaluate : 0.959 Fit side-chains REVERT: B 281 LYS cc_start: 0.5967 (mttm) cc_final: 0.5258 (mptt) REVERT: C 27 LYS cc_start: 0.7216 (mptt) cc_final: 0.6984 (mptt) REVERT: C 219 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4534 (mp0) REVERT: C 281 LYS cc_start: 0.6021 (mttm) cc_final: 0.5524 (mtmm) REVERT: C 294 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6511 (mm) REVERT: C 345 GLN cc_start: 0.7309 (pt0) cc_final: 0.7037 (pm20) REVERT: A 281 LYS cc_start: 0.6266 (mttm) cc_final: 0.5699 (mttp) outliers start: 63 outliers final: 42 residues processed: 210 average time/residue: 0.8816 time to fit residues: 200.0539 Evaluate side-chains 206 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8319 Z= 0.235 Angle : 0.710 9.201 11265 Z= 0.375 Chirality : 0.047 0.144 1128 Planarity : 0.004 0.056 1530 Dihedral : 5.505 53.699 1168 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.91 % Allowed : 29.82 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.25), residues: 1032 helix: -1.34 (0.84), residues: 42 sheet: -0.33 (0.22), residues: 543 loop : -2.49 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.017 0.002 PHE C 40 TYR 0.027 0.002 TYR C 98 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 0.837 Fit side-chains REVERT: B 281 LYS cc_start: 0.5878 (mttm) cc_final: 0.5165 (mptt) REVERT: C 27 LYS cc_start: 0.7199 (mptt) cc_final: 0.6929 (mptt) REVERT: C 219 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.4584 (mp0) REVERT: C 281 LYS cc_start: 0.5989 (mttm) cc_final: 0.5307 (mptt) REVERT: C 294 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6483 (mm) REVERT: C 345 GLN cc_start: 0.7269 (pt0) cc_final: 0.6961 (pm20) REVERT: A 281 LYS cc_start: 0.6224 (mttm) cc_final: 0.5483 (mptt) outliers start: 57 outliers final: 41 residues processed: 199 average time/residue: 0.8650 time to fit residues: 186.5418 Evaluate side-chains 195 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8319 Z= 0.357 Angle : 0.807 9.473 11265 Z= 0.431 Chirality : 0.050 0.193 1128 Planarity : 0.005 0.056 1530 Dihedral : 5.959 56.680 1168 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 7.27 % Allowed : 30.91 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.25), residues: 1032 helix: -1.75 (0.73), residues: 42 sheet: -0.34 (0.22), residues: 546 loop : -2.68 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.019 0.003 PHE C 40 TYR 0.030 0.003 TYR A 98 ARG 0.007 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 0.943 Fit side-chains REVERT: B 252 TRP cc_start: 0.6397 (OUTLIER) cc_final: 0.5139 (m-90) REVERT: B 281 LYS cc_start: 0.5825 (mttm) cc_final: 0.5080 (mptt) REVERT: C 27 LYS cc_start: 0.7230 (mptt) cc_final: 0.6716 (mmtp) REVERT: C 92 ARG cc_start: 0.6209 (tpt170) cc_final: 0.5996 (tpt170) REVERT: C 219 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.4501 (mp0) REVERT: C 281 LYS cc_start: 0.6109 (mttm) cc_final: 0.5410 (mttt) REVERT: C 294 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6576 (mm) REVERT: C 345 GLN cc_start: 0.7300 (pt0) cc_final: 0.7028 (pm20) REVERT: A 252 TRP cc_start: 0.6654 (OUTLIER) cc_final: 0.5246 (m-90) REVERT: A 281 LYS cc_start: 0.6307 (mttm) cc_final: 0.5719 (mttp) outliers start: 60 outliers final: 46 residues processed: 197 average time/residue: 0.8027 time to fit residues: 172.3553 Evaluate side-chains 204 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8319 Z= 0.223 Angle : 0.709 9.206 11265 Z= 0.376 Chirality : 0.047 0.136 1128 Planarity : 0.004 0.053 1530 Dihedral : 5.498 52.716 1168 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.70 % Allowed : 32.48 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 1032 helix: -1.26 (0.81), residues: 42 sheet: -0.30 (0.22), residues: 546 loop : -2.44 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 56 HIS 0.002 0.001 HIS A 21 PHE 0.017 0.002 PHE C 40 TYR 0.030 0.002 TYR B 98 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5843 (mttm) cc_final: 0.5130 (mptt) REVERT: C 27 LYS cc_start: 0.7148 (mptt) cc_final: 0.6905 (mptt) REVERT: C 219 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.4467 (mp0) REVERT: C 281 LYS cc_start: 0.5913 (mttm) cc_final: 0.5243 (mptt) REVERT: C 345 GLN cc_start: 0.7270 (pt0) cc_final: 0.6940 (pm20) REVERT: A 281 LYS cc_start: 0.6225 (mttm) cc_final: 0.5497 (mptt) outliers start: 47 outliers final: 40 residues processed: 191 average time/residue: 0.9197 time to fit residues: 189.8513 Evaluate side-chains 198 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 8319 Z= 0.425 Angle : 0.863 9.987 11265 Z= 0.463 Chirality : 0.051 0.205 1128 Planarity : 0.005 0.052 1530 Dihedral : 6.166 57.951 1168 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 6.79 % Allowed : 31.39 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.25), residues: 1032 helix: -1.89 (0.69), residues: 42 sheet: -0.33 (0.22), residues: 543 loop : -2.72 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 252 HIS 0.005 0.002 HIS A 21 PHE 0.020 0.003 PHE A 120 TYR 0.036 0.003 TYR A 98 ARG 0.007 0.001 ARG B 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 252 TRP cc_start: 0.6577 (OUTLIER) cc_final: 0.5161 (m-90) REVERT: B 281 LYS cc_start: 0.5920 (mttm) cc_final: 0.5194 (mptt) REVERT: C 27 LYS cc_start: 0.7209 (mptt) cc_final: 0.6685 (mmtp) REVERT: C 219 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.4533 (mp0) REVERT: C 281 LYS cc_start: 0.6072 (mttm) cc_final: 0.5576 (mtmm) REVERT: C 345 GLN cc_start: 0.7313 (pt0) cc_final: 0.7050 (pm20) REVERT: A 281 LYS cc_start: 0.6289 (mttm) cc_final: 0.5768 (mttp) outliers start: 56 outliers final: 46 residues processed: 196 average time/residue: 0.8433 time to fit residues: 180.0747 Evaluate side-chains 205 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 83 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.249702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.238404 restraints weight = 9614.046| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 1.77 r_work: 0.4687 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4600 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 8319 Z= 0.389 Angle : 1.131 59.197 11265 Z= 0.648 Chirality : 0.052 0.432 1128 Planarity : 0.005 0.053 1530 Dihedral : 6.229 57.768 1168 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 6.67 % Allowed : 31.64 % Favored : 61.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.25), residues: 1032 helix: -1.92 (0.69), residues: 42 sheet: -0.35 (0.22), residues: 543 loop : -2.73 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 252 HIS 0.004 0.002 HIS A 21 PHE 0.018 0.003 PHE A 120 TYR 0.035 0.003 TYR C 98 ARG 0.005 0.001 ARG B 174 =============================================================================== Job complete usr+sys time: 3368.78 seconds wall clock time: 61 minutes 17.56 seconds (3677.56 seconds total)