Starting phenix.real_space_refine on Sun Apr 5 03:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.map" model { file = "/net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ojk_70543/04_2026/9ojk_70543.cif" } resolution = 2.6 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= 0.017 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 39 5.16 5 C 4947 2.51 5 N 1275 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7743 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2508 Classifications: {'peptide': 321} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 305} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C Time building chain proxies: 1.33, per 1000 atoms: 0.17 Number of scatterers: 7743 At special positions: 0 Unit cell: (89.816, 84.048, 121.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 9 15.00 O 1473 8.00 N 1275 7.00 C 4947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " 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 Links applied NAG-ASN " NAG A 502 " - " ASN A 133 " " NAG A 503 " - " ASN A 310 " " NAG A 504 " - " ASN A 194 " " NAG B 502 " - " ASN B 133 " " NAG B 503 " - " ASN B 310 " " NAG B 504 " - " ASN B 194 " " NAG C 502 " - " ASN C 133 " " NAG C 503 " - " ASN C 310 " " NAG C 504 " - " ASN C 194 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 238.8 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 27.5% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 42 through 63 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.569A pdb=" N TYR A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.703A pdb=" N CYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 361 removed outlier: 3.990A pdb=" N GLY A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 63 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.569A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.702A pdb=" N CYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 351 through 361 removed outlier: 3.991A pdb=" N GLY B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 63 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.569A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.703A pdb=" N CYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 350 Processing helix chain 'C' and resid 351 through 361 removed outlier: 3.991A pdb=" N GLY C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 70 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 70 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 70 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 193 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2411 1.34 - 1.46: 1935 1.46 - 1.58: 3538 1.58 - 1.69: 15 1.69 - 1.81: 45 Bond restraints: 7944 Sorted by residual: bond pdb=" C VAL C 95 " pdb=" N GLU C 96 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.49e-02 4.50e+03 2.21e+00 bond pdb=" C VAL A 95 " pdb=" N GLU A 96 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.49e-02 4.50e+03 2.21e+00 bond pdb=" N GLU C 96 " pdb=" CA GLU C 96 " ideal model delta sigma weight residual 1.456 1.476 -0.019 1.31e-02 5.83e+03 2.14e+00 bond pdb=" C VAL B 95 " pdb=" N GLU B 96 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.49e-02 4.50e+03 2.13e+00 bond pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta sigma weight residual 1.456 1.476 -0.019 1.31e-02 5.83e+03 2.12e+00 ... (remaining 7939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 10361 1.15 - 2.30: 376 2.30 - 3.44: 57 3.44 - 4.59: 9 4.59 - 5.74: 9 Bond angle restraints: 10812 Sorted by residual: angle pdb=" CB GLU C 96 " pdb=" CG GLU C 96 " pdb=" CD GLU C 96 " ideal model delta sigma weight residual 112.60 118.34 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CB GLU B 96 " pdb=" CG GLU B 96 " pdb=" CD GLU B 96 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.70e+00 3.46e-01 1.13e+01 angle pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " pdb=" CD GLU A 96 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.70e+00 3.46e-01 1.12e+01 angle pdb=" C ILE B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.91e+00 angle pdb=" C ILE C 309 " pdb=" N ASN C 310 " pdb=" CA ASN C 310 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.90e+00 ... (remaining 10807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 4509 17.19 - 34.37: 213 34.37 - 51.56: 102 51.56 - 68.74: 21 68.74 - 85.93: 3 Dihedral angle restraints: 4848 sinusoidal: 2085 harmonic: 2763 Sorted by residual: dihedral pdb=" N PHE B 61 " pdb=" CA PHE B 61 " pdb=" CB PHE B 61 " pdb=" CG PHE B 61 " ideal model delta sinusoidal sigma weight residual -180.00 -121.82 -58.18 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N PHE C 61 " pdb=" CA PHE C 61 " pdb=" CB PHE C 61 " pdb=" CG PHE C 61 " ideal model delta sinusoidal sigma weight residual 180.00 -121.84 -58.16 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N PHE A 61 " pdb=" CA PHE A 61 " pdb=" CB PHE A 61 " pdb=" CG PHE A 61 " ideal model delta sinusoidal sigma weight residual -180.00 -121.87 -58.13 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 709 0.033 - 0.066: 320 0.066 - 0.099: 131 0.099 - 0.132: 64 0.132 - 0.165: 3 Chirality restraints: 1227 Sorted by residual: chirality pdb=" CA ASN C 310 " pdb=" N ASN C 310 " pdb=" C ASN C 310 " pdb=" CB ASN C 310 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ASN A 310 " pdb=" N ASN A 310 " pdb=" C ASN A 310 " pdb=" CB ASN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ASN B 310 " pdb=" N ASN B 310 " pdb=" C ASN B 310 " pdb=" CB ASN B 310 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1224 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 95 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C VAL B 95 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL B 95 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU B 96 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 95 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.60e+00 pdb=" C VAL A 95 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 95 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 96 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 95 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.60e+00 pdb=" C VAL C 95 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL C 95 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU C 96 " -0.007 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2216 2.82 - 3.34: 6695 3.34 - 3.86: 12903 3.86 - 4.38: 15086 4.38 - 4.90: 25932 Nonbonded interactions: 62832 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.295 3.040 nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.295 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.295 3.040 nonbonded pdb=" O SER C 70 " pdb=" NZ LYS C 207 " model vdw 2.345 3.120 nonbonded pdb=" O SER A 70 " pdb=" NZ LYS A 207 " model vdw 2.346 3.120 ... (remaining 62827 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: 0.02 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: 4.260 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.290 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.040 7968 Z= 0.213 Angle : 0.536 5.739 10869 Z= 0.283 Chirality : 0.048 0.165 1227 Planarity : 0.004 0.029 1338 Dihedral : 12.533 85.929 3045 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.82 % Allowed : 5.82 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 957 helix: -1.24 (0.33), residues: 192 sheet: 0.88 (0.28), residues: 327 loop : -0.86 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.011 0.001 TYR A 98 PHE 0.009 0.002 PHE C 336 TRP 0.014 0.002 TRP C 268 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 7944) covalent geometry : angle 0.52846 (10812) SS BOND : bond 0.00424 ( 15) SS BOND : angle 1.12373 ( 30) hydrogen bonds : bond 0.19559 ( 193) hydrogen bonds : angle 8.39322 ( 498) link_NAG-ASN : bond 0.00216 ( 9) link_NAG-ASN : angle 1.61814 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 97 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 158 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7433 (mtp85) REVERT: A 204 HIS cc_start: 0.7627 (t70) cc_final: 0.6940 (m-70) REVERT: B 56 PHE cc_start: 0.8133 (t80) cc_final: 0.7919 (t80) REVERT: B 61 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: B 233 ASP cc_start: 0.8000 (m-30) cc_final: 0.7787 (m-30) REVERT: B 250 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 354 VAL cc_start: 0.8375 (t) cc_final: 0.8147 (p) REVERT: C 61 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: C 115 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 191 MET cc_start: 0.7335 (mmm) cc_final: 0.6985 (mmm) REVERT: C 233 ASP cc_start: 0.7867 (m-30) cc_final: 0.7634 (m-30) REVERT: C 321 TYR cc_start: 0.8439 (m-80) cc_final: 0.8025 (m-80) outliers start: 15 outliers final: 2 residues processed: 257 average time/residue: 0.5453 time to fit residues: 147.6279 Evaluate side-chains 212 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.0470 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 201 ASN B 267 ASN C 152 ASN C 201 ASN C 344 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114437 restraints weight = 10918.811| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.00 r_work: 0.3422 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7968 Z= 0.131 Angle : 0.543 8.457 10869 Z= 0.278 Chirality : 0.048 0.160 1227 Planarity : 0.004 0.029 1338 Dihedral : 10.613 84.471 1340 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.79 % Allowed : 13.33 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.26), residues: 957 helix: -0.92 (0.33), residues: 201 sheet: 0.91 (0.28), residues: 327 loop : -0.98 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.010 0.001 TYR C 98 PHE 0.011 0.001 PHE C 243 TRP 0.010 0.001 TRP C 268 HIS 0.001 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7944) covalent geometry : angle 0.52970 (10812) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.78614 ( 30) hydrogen bonds : bond 0.03842 ( 193) hydrogen bonds : angle 5.97646 ( 498) link_NAG-ASN : bond 0.00437 ( 9) link_NAG-ASN : angle 2.38886 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: A 158 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7857 (mtp85) REVERT: A 204 HIS cc_start: 0.7671 (t70) cc_final: 0.6878 (m90) REVERT: A 289 ASP cc_start: 0.7886 (p0) cc_final: 0.7676 (p0) REVERT: B 56 PHE cc_start: 0.8121 (t80) cc_final: 0.7913 (t80) REVERT: B 61 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 96 GLU cc_start: 0.6901 (mp0) cc_final: 0.6691 (mp0) REVERT: B 250 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 61 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: C 127 GLU cc_start: 0.8056 (tp30) cc_final: 0.7843 (tp30) REVERT: C 130 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8301 (mtm-85) REVERT: C 152 ASN cc_start: 0.8592 (m-40) cc_final: 0.8331 (m-40) REVERT: C 168 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8388 (mtpt) REVERT: C 254 GLU cc_start: 0.7357 (pp20) cc_final: 0.7153 (pp20) outliers start: 23 outliers final: 5 residues processed: 226 average time/residue: 0.5362 time to fit residues: 128.0858 Evaluate side-chains 210 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 135 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113463 restraints weight = 10890.866| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3407 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7968 Z= 0.201 Angle : 0.571 8.766 10869 Z= 0.293 Chirality : 0.049 0.172 1227 Planarity : 0.004 0.035 1338 Dihedral : 10.403 83.823 1338 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 15.39 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 957 helix: -0.79 (0.33), residues: 201 sheet: 0.88 (0.28), residues: 327 loop : -1.01 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 286 TYR 0.013 0.002 TYR C 235 PHE 0.012 0.002 PHE C 243 TRP 0.014 0.001 TRP C 268 HIS 0.002 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 7944) covalent geometry : angle 0.55751 (10812) SS BOND : bond 0.00380 ( 15) SS BOND : angle 1.10937 ( 30) hydrogen bonds : bond 0.03939 ( 193) hydrogen bonds : angle 6.12673 ( 498) link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 2.30733 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 158 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7918 (mtp85) REVERT: A 204 HIS cc_start: 0.7678 (t70) cc_final: 0.6947 (m90) REVERT: A 233 ASP cc_start: 0.8176 (m-30) cc_final: 0.7964 (m-30) REVERT: A 289 ASP cc_start: 0.7878 (p0) cc_final: 0.7643 (p0) REVERT: B 56 PHE cc_start: 0.8120 (t80) cc_final: 0.7912 (t80) REVERT: B 224 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8259 (mtpp) REVERT: B 254 GLU cc_start: 0.7439 (mp0) cc_final: 0.7193 (mp0) REVERT: C 61 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: C 152 ASN cc_start: 0.8642 (m-40) cc_final: 0.8395 (m-40) REVERT: C 233 ASP cc_start: 0.8069 (m-30) cc_final: 0.7791 (m-30) REVERT: C 278 GLU cc_start: 0.8424 (mp0) cc_final: 0.8214 (mm-30) outliers start: 25 outliers final: 14 residues processed: 227 average time/residue: 0.5492 time to fit residues: 131.5769 Evaluate side-chains 224 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 362 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113926 restraints weight = 10931.584| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.00 r_work: 0.3393 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7968 Z= 0.171 Angle : 0.566 9.742 10869 Z= 0.286 Chirality : 0.049 0.168 1227 Planarity : 0.004 0.046 1338 Dihedral : 10.122 87.682 1338 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.15 % Allowed : 16.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 957 helix: -0.61 (0.34), residues: 201 sheet: 0.86 (0.28), residues: 327 loop : -0.99 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 286 TYR 0.014 0.001 TYR C 98 PHE 0.012 0.001 PHE C 56 TRP 0.012 0.001 TRP C 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7944) covalent geometry : angle 0.55021 (10812) SS BOND : bond 0.00349 ( 15) SS BOND : angle 1.04711 ( 30) hydrogen bonds : bond 0.03568 ( 193) hydrogen bonds : angle 6.03115 ( 498) link_NAG-ASN : bond 0.00287 ( 9) link_NAG-ASN : angle 2.51977 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 VAL cc_start: 0.8057 (t) cc_final: 0.7857 (p) REVERT: A 61 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: A 158 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7876 (mtp85) REVERT: A 204 HIS cc_start: 0.7687 (t70) cc_final: 0.6967 (m90) REVERT: A 289 ASP cc_start: 0.7884 (p0) cc_final: 0.7673 (p0) REVERT: B 56 PHE cc_start: 0.8130 (t80) cc_final: 0.7927 (t80) REVERT: B 254 GLU cc_start: 0.7488 (mp0) cc_final: 0.7268 (mp0) REVERT: C 61 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: C 278 GLU cc_start: 0.8387 (mp0) cc_final: 0.8186 (mm-30) outliers start: 26 outliers final: 11 residues processed: 224 average time/residue: 0.5543 time to fit residues: 130.9524 Evaluate side-chains 212 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113962 restraints weight = 10858.066| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.00 r_work: 0.3413 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7968 Z= 0.180 Angle : 0.576 8.577 10869 Z= 0.292 Chirality : 0.049 0.169 1227 Planarity : 0.004 0.055 1338 Dihedral : 10.081 86.061 1338 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.27 % Allowed : 17.33 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.26), residues: 957 helix: -0.55 (0.34), residues: 201 sheet: 0.84 (0.28), residues: 327 loop : -0.98 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 286 TYR 0.015 0.001 TYR C 98 PHE 0.014 0.001 PHE A 56 TRP 0.011 0.001 TRP C 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7944) covalent geometry : angle 0.55597 (10812) SS BOND : bond 0.00364 ( 15) SS BOND : angle 1.12550 ( 30) hydrogen bonds : bond 0.03562 ( 193) hydrogen bonds : angle 6.01747 ( 498) link_NAG-ASN : bond 0.00474 ( 9) link_NAG-ASN : angle 2.86902 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: A 158 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7875 (mtp85) REVERT: A 204 HIS cc_start: 0.7683 (t70) cc_final: 0.6961 (m90) REVERT: A 238 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7953 (mm) REVERT: B 56 PHE cc_start: 0.8115 (t80) cc_final: 0.7910 (t80) REVERT: C 61 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: C 152 ASN cc_start: 0.8644 (m-40) cc_final: 0.8386 (m-40) REVERT: C 278 GLU cc_start: 0.8396 (mp0) cc_final: 0.8186 (mm-30) outliers start: 27 outliers final: 15 residues processed: 220 average time/residue: 0.5545 time to fit residues: 128.6196 Evaluate side-chains 215 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 347 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113857 restraints weight = 10919.900| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.98 r_work: 0.3391 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7968 Z= 0.198 Angle : 0.610 9.229 10869 Z= 0.305 Chirality : 0.050 0.176 1227 Planarity : 0.005 0.055 1338 Dihedral : 10.127 83.246 1338 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.03 % Allowed : 18.06 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 957 helix: -0.56 (0.34), residues: 201 sheet: 0.84 (0.28), residues: 327 loop : -0.98 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 286 TYR 0.016 0.001 TYR C 98 PHE 0.010 0.002 PHE C 243 TRP 0.011 0.001 TRP A 268 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 7944) covalent geometry : angle 0.58324 (10812) SS BOND : bond 0.00375 ( 15) SS BOND : angle 1.19717 ( 30) hydrogen bonds : bond 0.03646 ( 193) hydrogen bonds : angle 6.06219 ( 498) link_NAG-ASN : bond 0.00297 ( 9) link_NAG-ASN : angle 3.45509 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: A 158 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7885 (mtp85) REVERT: A 204 HIS cc_start: 0.7691 (t70) cc_final: 0.6988 (m90) REVERT: A 238 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 289 ASP cc_start: 0.7952 (p0) cc_final: 0.7706 (p0) REVERT: B 56 PHE cc_start: 0.8124 (t80) cc_final: 0.7918 (t80) REVERT: C 61 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 25 outliers final: 18 residues processed: 215 average time/residue: 0.5612 time to fit residues: 127.3462 Evaluate side-chains 219 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 347 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114135 restraints weight = 10895.077| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.97 r_work: 0.3425 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7968 Z= 0.145 Angle : 0.586 8.731 10869 Z= 0.293 Chirality : 0.048 0.191 1227 Planarity : 0.004 0.037 1338 Dihedral : 10.031 82.521 1338 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.42 % Allowed : 19.88 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 957 helix: -0.43 (0.34), residues: 201 sheet: 0.87 (0.28), residues: 327 loop : -0.96 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 286 TYR 0.012 0.001 TYR A 98 PHE 0.008 0.001 PHE C 243 TRP 0.010 0.001 TRP C 268 HIS 0.001 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7944) covalent geometry : angle 0.56091 (10812) SS BOND : bond 0.00305 ( 15) SS BOND : angle 0.93339 ( 30) hydrogen bonds : bond 0.03397 ( 193) hydrogen bonds : angle 5.93906 ( 498) link_NAG-ASN : bond 0.00375 ( 9) link_NAG-ASN : angle 3.38109 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 VAL cc_start: 0.8059 (t) cc_final: 0.7851 (p) REVERT: A 61 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: A 158 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7787 (mtp85) REVERT: A 204 HIS cc_start: 0.7668 (t70) cc_final: 0.6914 (m90) REVERT: A 238 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 289 ASP cc_start: 0.7953 (p0) cc_final: 0.7718 (p0) REVERT: B 61 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: C 61 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: C 152 ASN cc_start: 0.8633 (m-40) cc_final: 0.8391 (m-40) outliers start: 20 outliers final: 9 residues processed: 216 average time/residue: 0.5293 time to fit residues: 120.8108 Evaluate side-chains 215 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 347 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115720 restraints weight = 10976.728| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.99 r_work: 0.3441 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7968 Z= 0.109 Angle : 0.590 9.245 10869 Z= 0.289 Chirality : 0.048 0.168 1227 Planarity : 0.004 0.052 1338 Dihedral : 9.885 88.847 1338 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.06 % Allowed : 21.09 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 957 helix: -0.20 (0.35), residues: 201 sheet: 0.75 (0.28), residues: 333 loop : -0.96 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.009 0.001 TYR A 98 PHE 0.011 0.001 PHE C 56 TRP 0.007 0.001 TRP B 268 HIS 0.001 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7944) covalent geometry : angle 0.56733 (10812) SS BOND : bond 0.00248 ( 15) SS BOND : angle 0.74410 ( 30) hydrogen bonds : bond 0.02987 ( 193) hydrogen bonds : angle 5.80542 ( 498) link_NAG-ASN : bond 0.00481 ( 9) link_NAG-ASN : angle 3.28319 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 158 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7803 (mtp85) REVERT: A 204 HIS cc_start: 0.7654 (t70) cc_final: 0.6869 (m90) REVERT: A 238 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 271 ASP cc_start: 0.7935 (t0) cc_final: 0.7714 (t70) REVERT: A 289 ASP cc_start: 0.7943 (p0) cc_final: 0.7696 (p0) REVERT: B 61 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: C 61 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7830 (m-80) outliers start: 17 outliers final: 7 residues processed: 209 average time/residue: 0.4966 time to fit residues: 110.0970 Evaluate side-chains 205 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113950 restraints weight = 10974.708| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.98 r_work: 0.3415 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7968 Z= 0.186 Angle : 0.637 10.192 10869 Z= 0.312 Chirality : 0.050 0.208 1227 Planarity : 0.004 0.051 1338 Dihedral : 10.117 89.380 1338 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.06 % Allowed : 21.21 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 957 helix: -0.28 (0.35), residues: 201 sheet: 0.87 (0.28), residues: 327 loop : -0.97 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 286 TYR 0.016 0.001 TYR C 98 PHE 0.024 0.002 PHE B 56 TRP 0.010 0.001 TRP A 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7944) covalent geometry : angle 0.60397 (10812) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.18943 ( 30) hydrogen bonds : bond 0.03515 ( 193) hydrogen bonds : angle 5.98903 ( 498) link_NAG-ASN : bond 0.00418 ( 9) link_NAG-ASN : angle 3.98290 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: A 158 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7804 (mtp85) REVERT: A 204 HIS cc_start: 0.7665 (t70) cc_final: 0.6931 (m90) REVERT: A 238 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7985 (mm) REVERT: A 289 ASP cc_start: 0.7924 (p0) cc_final: 0.7693 (p0) REVERT: B 61 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: C 61 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: C 152 ASN cc_start: 0.8589 (m-40) cc_final: 0.8359 (m-40) outliers start: 17 outliers final: 9 residues processed: 206 average time/residue: 0.5319 time to fit residues: 115.9302 Evaluate side-chains 208 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113972 restraints weight = 10894.387| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.97 r_work: 0.3415 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7968 Z= 0.185 Angle : 0.649 11.927 10869 Z= 0.314 Chirality : 0.049 0.168 1227 Planarity : 0.004 0.047 1338 Dihedral : 10.304 88.634 1338 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.70 % Allowed : 21.70 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 957 helix: -0.37 (0.34), residues: 201 sheet: 0.87 (0.28), residues: 327 loop : -0.94 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 286 TYR 0.016 0.001 TYR C 98 PHE 0.010 0.001 PHE C 56 TRP 0.009 0.001 TRP C 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7944) covalent geometry : angle 0.60910 (10812) SS BOND : bond 0.00356 ( 15) SS BOND : angle 1.13454 ( 30) hydrogen bonds : bond 0.03483 ( 193) hydrogen bonds : angle 6.05028 ( 498) link_NAG-ASN : bond 0.00524 ( 9) link_NAG-ASN : angle 4.40212 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: A 158 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7816 (mtp85) REVERT: A 204 HIS cc_start: 0.7676 (t70) cc_final: 0.6936 (m90) REVERT: A 238 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 289 ASP cc_start: 0.7934 (p0) cc_final: 0.7698 (p0) REVERT: B 61 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: C 61 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: C 233 ASP cc_start: 0.8027 (m-30) cc_final: 0.7728 (m-30) outliers start: 14 outliers final: 10 residues processed: 206 average time/residue: 0.5261 time to fit residues: 114.5750 Evaluate side-chains 213 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 135 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 267 ASN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114069 restraints weight = 10970.294| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.98 r_work: 0.3414 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7968 Z= 0.172 Angle : 0.628 11.277 10869 Z= 0.307 Chirality : 0.049 0.168 1227 Planarity : 0.004 0.046 1338 Dihedral : 10.147 88.798 1338 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 21.94 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 957 helix: -0.28 (0.35), residues: 201 sheet: 0.88 (0.28), residues: 327 loop : -0.93 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 286 TYR 0.015 0.001 TYR C 98 PHE 0.024 0.001 PHE B 56 TRP 0.010 0.001 TRP C 268 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7944) covalent geometry : angle 0.60450 (10812) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.07791 ( 30) hydrogen bonds : bond 0.03447 ( 193) hydrogen bonds : angle 6.03387 ( 498) link_NAG-ASN : bond 0.00350 ( 9) link_NAG-ASN : angle 3.32666 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.73 seconds wall clock time: 57 minutes 56.67 seconds (3476.67 seconds total)