Starting phenix.real_space_refine on Sat Aug 23 12:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unk_42407/08_2025/8unk_42407.map" } resolution = 2.91 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2715 atoms to isotropic. 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 S 22 5.16 5 C 3257 2.51 5 N 877 2.21 5 O 913 1.98 5 H 4793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9862 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2612 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 7, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1954 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 9, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "K" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4587 Classifications: {'peptide': 317} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 302} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 709 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.33, per 1000 atoms: 0.24 Number of scatterers: 9862 At special positions: 0 Unit cell: (64.35, 69.3, 133.65, 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 22 16.00 O 913 8.00 N 877 7.00 C 3257 6.00 H 4793 1.00 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 - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 253.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1288 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 57.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 369 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.633A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 Processing helix chain 'B' and resid 498 through 514 Processing helix chain 'B' and resid 516 through 529 removed outlier: 3.590A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.816A pdb=" N LEU C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'K' and resid 43 through 63 Proline residue: K 53 - end of helix Processing helix chain 'K' and resid 64 through 68 removed outlier: 3.508A pdb=" N ILE K 68 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 153 through 165 Processing helix chain 'K' and resid 171 through 180 Processing helix chain 'K' and resid 198 through 212 removed outlier: 3.866A pdb=" N LEU K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 243 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 256 through 270 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.533A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 4.027A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 315 through 319 removed outlier: 3.512A pdb=" N VAL K 319 " --> pdb=" O THR K 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 32 removed outlier: 4.104A pdb=" N ALA P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 79 Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 361 Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AA4, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.611A pdb=" N VAL C 86 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG C 12 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 88 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY C 10 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS C 90 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE C 8 " --> pdb=" O CYS C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 26 through 31 removed outlier: 6.902A pdb=" N ILE K 2 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA K 72 " --> pdb=" O ILE K 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU K 4 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER K 74 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU K 6 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY K 76 " --> pdb=" O LEU K 6 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE K 71 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL K 104 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE K 73 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 142 through 148 removed outlier: 5.621A pdb=" N VAL K 135 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU K 148 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR K 133 " --> pdb=" O GLU K 148 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU K 124 " --> pdb=" O MET K 248 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL K 250 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU K 126 " --> pdb=" O VAL K 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193 310 hydrogen bonds defined for protein. 876 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: 2.42 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4786 1.03 - 1.23: 16 1.23 - 1.42: 2095 1.42 - 1.62: 3013 1.62 - 1.81: 37 Bond restraints: 9947 Sorted by residual: bond pdb=" N MET K 1 " pdb=" H1 MET K 1 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C PRO K 173 " pdb=" O PRO K 173 " ideal model delta sigma weight residual 1.238 1.211 0.027 1.24e-02 6.50e+03 4.62e+00 bond pdb=" C GLY K 172 " pdb=" N PRO K 173 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.80e+00 bond pdb=" CB MET K 230 " pdb=" CG MET K 230 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CA PRO K 173 " pdb=" C PRO K 173 " ideal model delta sigma weight residual 1.516 1.535 -0.019 1.61e-02 3.86e+03 1.37e+00 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 17078 1.20 - 2.39: 778 2.39 - 3.59: 57 3.59 - 4.79: 10 4.79 - 5.98: 2 Bond angle restraints: 17925 Sorted by residual: angle pdb=" N ASN K 322 " pdb=" CA ASN K 322 " pdb=" C ASN K 322 " ideal model delta sigma weight residual 114.56 110.24 4.32 1.27e+00 6.20e-01 1.16e+01 angle pdb=" CB ARG C 120 " pdb=" CG ARG C 120 " pdb=" CD ARG C 120 " ideal model delta sigma weight residual 111.30 116.93 -5.63 2.30e+00 1.89e-01 5.99e+00 angle pdb=" CG ARG C 120 " pdb=" CD ARG C 120 " pdb=" NE ARG C 120 " ideal model delta sigma weight residual 112.00 116.66 -4.66 2.20e+00 2.07e-01 4.49e+00 angle pdb=" N LYS P 44 " pdb=" CA LYS P 44 " pdb=" C LYS P 44 " ideal model delta sigma weight residual 108.24 110.99 -2.75 1.32e+00 5.74e-01 4.34e+00 angle pdb=" C GLY K 172 " pdb=" N PRO K 173 " pdb=" CA PRO K 173 " ideal model delta sigma weight residual 119.28 121.56 -2.28 1.10e+00 8.26e-01 4.31e+00 ... (remaining 17920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4134 17.68 - 35.36: 396 35.36 - 53.04: 135 53.04 - 70.72: 30 70.72 - 88.40: 4 Dihedral angle restraints: 4699 sinusoidal: 2410 harmonic: 2289 Sorted by residual: dihedral pdb=" CB GLU K 177 " pdb=" CG GLU K 177 " pdb=" CD GLU K 177 " pdb=" OE1 GLU K 177 " ideal model delta sinusoidal sigma weight residual 0.00 88.40 -88.40 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU K 124 " pdb=" C LEU K 124 " pdb=" N THR K 125 " pdb=" CA THR K 125 " ideal model delta harmonic sigma weight residual -180.00 -163.94 -16.06 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CG ARG K 208 " pdb=" CD ARG K 208 " pdb=" NE ARG K 208 " pdb=" CZ ARG K 208 " ideal model delta sinusoidal sigma weight residual 90.00 132.65 -42.65 2 1.50e+01 4.44e-03 9.79e+00 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 536 0.029 - 0.058: 179 0.058 - 0.087: 66 0.087 - 0.116: 43 0.116 - 0.145: 13 Chirality restraints: 837 Sorted by residual: chirality pdb=" CB VAL C 138 " pdb=" CA VAL C 138 " pdb=" CG1 VAL C 138 " pdb=" CG2 VAL C 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE C 89 " pdb=" N ILE C 89 " pdb=" C ILE C 89 " pdb=" CB ILE C 89 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE B 396 " pdb=" N ILE B 396 " pdb=" C ILE B 396 " pdb=" CB ILE B 396 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 834 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 173 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" N TYR K 174 " 0.041 2.00e-02 2.50e+03 pdb=" CA TYR K 174 " -0.010 2.00e-02 2.50e+03 pdb=" H TYR K 174 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 33 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO K 34 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO K 34 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 34 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 74 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C LYS P 74 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS P 74 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA P 75 " 0.008 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.81: 51 1.81 - 2.50: 7781 2.50 - 3.20: 31493 3.20 - 3.90: 40366 3.90 - 4.60: 62727 Nonbonded interactions: 142418 Sorted by model distance: nonbonded pdb="HD13 ILE B 465 " pdb=" HE1 PHE B 468 " model vdw 1.107 2.270 nonbonded pdb=" HG LEU B 388 " pdb=" HD2 PHE B 468 " model vdw 1.136 2.270 nonbonded pdb=" OH TYR K 314 " pdb=" CG2 VAL K 319 " model vdw 1.226 3.100 nonbonded pdb=" HH TYR K 314 " pdb=" CG2 VAL K 319 " model vdw 1.227 2.750 nonbonded pdb=" HB2 ASN K 105 " pdb=" HE2 TYR K 314 " model vdw 1.234 2.270 ... (remaining 142413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 5155 Z= 0.357 Angle : 0.550 5.631 7003 Z= 0.318 Chirality : 0.041 0.145 837 Planarity : 0.004 0.043 889 Dihedral : 15.980 88.402 1769 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 26.22 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.18 (0.34), residues: 673 helix: 1.23 (0.29), residues: 358 sheet: -0.34 (0.63), residues: 69 loop : -1.39 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 120 TYR 0.010 0.001 TYR K 190 PHE 0.016 0.001 PHE K 60 TRP 0.009 0.001 TRP C 59 HIS 0.003 0.001 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5154) covalent geometry : angle 0.54976 ( 7003) hydrogen bonds : bond 0.11957 ( 310) hydrogen bonds : angle 6.50171 ( 876) Misc. bond : bond 0.23357 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 LYS cc_start: 0.8469 (mppt) cc_final: 0.8066 (mmmm) REVERT: K 140 SER cc_start: 0.8427 (m) cc_final: 0.8220 (p) REVERT: K 288 MET cc_start: 0.6167 (ptt) cc_final: 0.5819 (ptt) REVERT: P 78 ASP cc_start: 0.6797 (m-30) cc_final: 0.6419 (m-30) outliers start: 0 outliers final: 1 residues processed: 104 average time/residue: 0.8306 time to fit residues: 91.6520 Evaluate side-chains 91 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 299 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.162123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.135878 restraints weight = 22553.191| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.17 r_work: 0.4195 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5155 Z= 0.156 Angle : 0.532 4.984 7003 Z= 0.295 Chirality : 0.041 0.138 837 Planarity : 0.004 0.040 889 Dihedral : 4.345 25.348 737 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.38 % Allowed : 27.27 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.21 (0.33), residues: 673 helix: 1.43 (0.28), residues: 352 sheet: -0.64 (0.62), residues: 69 loop : -1.51 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 208 TYR 0.019 0.002 TYR K 314 PHE 0.013 0.001 PHE K 274 TRP 0.009 0.001 TRP C 59 HIS 0.004 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5154) covalent geometry : angle 0.53240 ( 7003) hydrogen bonds : bond 0.03799 ( 310) hydrogen bonds : angle 5.60457 ( 876) Misc. bond : bond 0.00369 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASN cc_start: 0.8442 (m-40) cc_final: 0.8188 (t0) REVERT: C 56 LYS cc_start: 0.8427 (mppt) cc_final: 0.7973 (mmmm) REVERT: P 78 ASP cc_start: 0.7725 (m-30) cc_final: 0.7282 (m-30) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.8132 time to fit residues: 85.6518 Evaluate side-chains 90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 241 HIS Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 317 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 59 optimal weight: 0.9980 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN K 75 GLN K 169 HIS K 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.162370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.135933 restraints weight = 22587.773| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 3.18 r_work: 0.4193 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5155 Z= 0.146 Angle : 0.517 5.055 7003 Z= 0.286 Chirality : 0.041 0.134 837 Planarity : 0.004 0.039 889 Dihedral : 4.316 32.734 737 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.86 % Allowed : 26.22 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.31 (0.33), residues: 673 helix: 1.59 (0.28), residues: 353 sheet: -0.75 (0.65), residues: 67 loop : -1.54 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 208 TYR 0.016 0.002 TYR K 314 PHE 0.013 0.001 PHE K 274 TRP 0.008 0.001 TRP C 59 HIS 0.006 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5154) covalent geometry : angle 0.51713 ( 7003) hydrogen bonds : bond 0.03547 ( 310) hydrogen bonds : angle 5.35408 ( 876) Misc. bond : bond 0.00567 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7826 (p0) REVERT: B 524 MET cc_start: 0.6625 (ttt) cc_final: 0.6409 (ttt) REVERT: C 56 LYS cc_start: 0.8348 (mppt) cc_final: 0.7902 (mmmm) REVERT: P 78 ASP cc_start: 0.7848 (m-30) cc_final: 0.7244 (m-30) outliers start: 23 outliers final: 10 residues processed: 111 average time/residue: 0.7504 time to fit residues: 89.0107 Evaluate side-chains 90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 241 HIS Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 317 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN K 169 HIS K 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.163301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.137216 restraints weight = 22705.613| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 3.17 r_work: 0.4237 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5155 Z= 0.138 Angle : 0.521 5.545 7003 Z= 0.286 Chirality : 0.041 0.147 837 Planarity : 0.004 0.038 889 Dihedral : 4.021 17.247 735 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.44 % Allowed : 28.54 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.38 (0.33), residues: 673 helix: 1.60 (0.28), residues: 354 sheet: -0.65 (0.66), residues: 66 loop : -1.48 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 208 TYR 0.012 0.001 TYR K 314 PHE 0.012 0.001 PHE K 274 TRP 0.007 0.001 TRP C 59 HIS 0.008 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5154) covalent geometry : angle 0.52139 ( 7003) hydrogen bonds : bond 0.03347 ( 310) hydrogen bonds : angle 5.18863 ( 876) Misc. bond : bond 0.00475 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7816 (p0) REVERT: C 56 LYS cc_start: 0.8318 (mppt) cc_final: 0.7854 (mmmm) REVERT: K 60 PHE cc_start: 0.5444 (m-10) cc_final: 0.5199 (m-10) REVERT: K 75 GLN cc_start: 0.5350 (tt0) cc_final: 0.5010 (tp-100) REVERT: K 197 ILE cc_start: 0.8309 (mt) cc_final: 0.8010 (mp) REVERT: P 78 ASP cc_start: 0.7828 (m-30) cc_final: 0.7383 (m-30) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.7369 time to fit residues: 82.8288 Evaluate side-chains 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 241 HIS Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 317 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN K 169 HIS ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.160564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.134026 restraints weight = 22792.234| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 3.20 r_work: 0.4161 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5155 Z= 0.165 Angle : 0.533 5.506 7003 Z= 0.294 Chirality : 0.041 0.134 837 Planarity : 0.004 0.038 889 Dihedral : 4.093 17.681 735 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.65 % Allowed : 27.70 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.23 (0.33), residues: 673 helix: 1.44 (0.28), residues: 355 sheet: -0.60 (0.69), residues: 66 loop : -1.52 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 208 TYR 0.015 0.002 TYR K 190 PHE 0.014 0.001 PHE K 274 TRP 0.009 0.001 TRP B 517 HIS 0.013 0.002 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5154) covalent geometry : angle 0.53310 ( 7003) hydrogen bonds : bond 0.03482 ( 310) hydrogen bonds : angle 5.12652 ( 876) Misc. bond : bond 0.00513 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 LYS cc_start: 0.8288 (mppt) cc_final: 0.7808 (mmmm) REVERT: P 78 ASP cc_start: 0.7784 (m-30) cc_final: 0.7431 (m-30) outliers start: 22 outliers final: 10 residues processed: 105 average time/residue: 0.7847 time to fit residues: 87.8912 Evaluate side-chains 94 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 241 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.162332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.136176 restraints weight = 22695.875| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 3.16 r_work: 0.4218 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5155 Z= 0.141 Angle : 0.530 5.789 7003 Z= 0.289 Chirality : 0.041 0.139 837 Planarity : 0.004 0.057 889 Dihedral : 4.043 17.421 735 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.44 % Allowed : 28.75 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.28 (0.33), residues: 673 helix: 1.50 (0.28), residues: 355 sheet: -0.53 (0.68), residues: 65 loop : -1.55 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 208 TYR 0.018 0.002 TYR P 69 PHE 0.013 0.001 PHE K 274 TRP 0.007 0.001 TRP C 59 HIS 0.013 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5154) covalent geometry : angle 0.52996 ( 7003) hydrogen bonds : bond 0.03294 ( 310) hydrogen bonds : angle 5.04768 ( 876) Misc. bond : bond 0.00456 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: K 75 GLN cc_start: 0.5329 (tt0) cc_final: 0.5092 (tp-100) REVERT: K 197 ILE cc_start: 0.8348 (mt) cc_final: 0.8101 (mp) REVERT: P 78 ASP cc_start: 0.7742 (m-30) cc_final: 0.7490 (m-30) outliers start: 21 outliers final: 12 residues processed: 106 average time/residue: 0.7985 time to fit residues: 90.4722 Evaluate side-chains 100 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 241 HIS Chi-restraints excluded: chain K residue 273 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.158628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.132293 restraints weight = 22913.504| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.17 r_work: 0.4137 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5155 Z= 0.191 Angle : 0.563 6.340 7003 Z= 0.310 Chirality : 0.042 0.149 837 Planarity : 0.004 0.064 889 Dihedral : 4.207 17.779 735 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.65 % Allowed : 28.96 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: -0.01 (0.33), residues: 673 helix: 1.23 (0.27), residues: 355 sheet: -0.82 (0.63), residues: 75 loop : -1.60 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 120 TYR 0.017 0.002 TYR K 190 PHE 0.034 0.002 PHE C 21 TRP 0.009 0.002 TRP B 517 HIS 0.014 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5154) covalent geometry : angle 0.56276 ( 7003) hydrogen bonds : bond 0.03604 ( 310) hydrogen bonds : angle 5.14655 ( 876) Misc. bond : bond 0.00526 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 75 GLN cc_start: 0.5424 (tt0) cc_final: 0.5003 (tp-100) REVERT: K 106 HIS cc_start: 0.5714 (t-170) cc_final: 0.5466 (t-170) REVERT: P 78 ASP cc_start: 0.7845 (m-30) cc_final: 0.7610 (m-30) outliers start: 22 outliers final: 15 residues processed: 105 average time/residue: 0.6708 time to fit residues: 75.6969 Evaluate side-chains 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 310 ILE Chi-restraints excluded: chain K residue 317 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 65 optimal weight: 0.0770 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.163843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.137726 restraints weight = 22485.432| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.16 r_work: 0.4238 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5155 Z= 0.118 Angle : 0.535 5.645 7003 Z= 0.290 Chirality : 0.041 0.156 837 Planarity : 0.005 0.079 889 Dihedral : 4.009 16.714 735 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.17 % Allowed : 30.87 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.28 (0.33), residues: 673 helix: 1.50 (0.28), residues: 355 sheet: -0.57 (0.67), residues: 65 loop : -1.54 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 208 TYR 0.018 0.001 TYR P 69 PHE 0.011 0.001 PHE K 274 TRP 0.008 0.001 TRP C 59 HIS 0.011 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5154) covalent geometry : angle 0.53469 ( 7003) hydrogen bonds : bond 0.03147 ( 310) hydrogen bonds : angle 4.80847 ( 876) Misc. bond : bond 0.00382 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 75 GLN cc_start: 0.5287 (tt0) cc_final: 0.4949 (tp-100) REVERT: P 78 ASP cc_start: 0.7697 (m-30) cc_final: 0.7430 (m-30) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.8020 time to fit residues: 85.1689 Evaluate side-chains 94 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.163588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.137542 restraints weight = 22686.419| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.17 r_work: 0.4232 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5155 Z= 0.133 Angle : 0.537 5.732 7003 Z= 0.292 Chirality : 0.041 0.160 837 Planarity : 0.005 0.101 889 Dihedral : 3.954 16.792 735 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.11 % Allowed : 31.29 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.32 (0.33), residues: 673 helix: 1.53 (0.28), residues: 357 sheet: -0.56 (0.67), residues: 65 loop : -1.54 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.017 0.002 TYR K 32 PHE 0.031 0.001 PHE C 21 TRP 0.007 0.001 TRP C 59 HIS 0.012 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5154) covalent geometry : angle 0.53678 ( 7003) hydrogen bonds : bond 0.03149 ( 310) hydrogen bonds : angle 4.81025 ( 876) Misc. bond : bond 0.00432 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 75 GLN cc_start: 0.5351 (tt0) cc_final: 0.4914 (tp-100) REVERT: K 197 ILE cc_start: 0.8381 (mt) cc_final: 0.8129 (mp) REVERT: P 78 ASP cc_start: 0.7710 (m-30) cc_final: 0.7496 (m-30) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.7525 time to fit residues: 78.1272 Evaluate side-chains 91 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.137732 restraints weight = 22506.715| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.19 r_work: 0.4238 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5155 Z= 0.128 Angle : 0.539 5.759 7003 Z= 0.293 Chirality : 0.041 0.166 837 Planarity : 0.005 0.099 889 Dihedral : 3.892 16.554 735 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 31.08 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.34 (0.33), residues: 673 helix: 1.52 (0.28), residues: 358 sheet: -0.66 (0.67), residues: 65 loop : -1.45 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.020 0.001 TYR P 69 PHE 0.012 0.001 PHE K 274 TRP 0.007 0.001 TRP K 302 HIS 0.004 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5154) covalent geometry : angle 0.53917 ( 7003) hydrogen bonds : bond 0.03107 ( 310) hydrogen bonds : angle 4.75142 ( 876) Misc. bond : bond 0.00406 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LYS 444 is missing expected H atoms. Skipping. Residue LYS 461 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue LYS 488 is missing expected H atoms. Skipping. Residue LYS 489 is missing expected H atoms. Skipping. Residue ILE 519 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue VAL 527 is missing expected H atoms. Skipping. Residue ILE 8 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue ILE 76 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 19 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 141 is missing expected H atoms. Skipping. Residue LYS 181 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue MET 248 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue VAL 319 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue SER 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue ILE 73 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 75 GLN cc_start: 0.5325 (tt0) cc_final: 0.4901 (tp-100) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.7491 time to fit residues: 75.9168 Evaluate side-chains 92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** K 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.163550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.137729 restraints weight = 22742.582| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.18 r_work: 0.4237 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 5155 Z= 0.238 Angle : 1.034 59.156 7003 Z= 0.642 Chirality : 0.048 0.726 837 Planarity : 0.005 0.100 889 Dihedral : 3.954 18.950 735 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 31.50 % Favored : 66.17 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 10.53 % 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 aren not related in a simple way. whole: 0.34 (0.33), residues: 673 helix: 1.51 (0.28), residues: 358 sheet: -0.67 (0.67), residues: 65 loop : -1.45 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 120 TYR 0.019 0.002 TYR P 69 PHE 0.012 0.001 PHE K 274 TRP 0.006 0.001 TRP C 59 HIS 0.004 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 5154) covalent geometry : angle 1.03428 ( 7003) hydrogen bonds : bond 0.03112 ( 310) hydrogen bonds : angle 4.76999 ( 876) Misc. bond : bond 0.00426 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.72 seconds wall clock time: 62 minutes 57.35 seconds (3777.35 seconds total)