Starting phenix.real_space_refine on Wed May 14 15:55:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unk_42407/05_2025/8unk_42407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unk_42407/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8unk_42407/05_2025/8unk_42407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unk_42407/05_2025/8unk_42407.map" model { file = "/net/cci-nas-00/data/ceres_data/8unk_42407/05_2025/8unk_42407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unk_42407/05_2025/8unk_42407.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 9} 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: {'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 3, '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: {'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 4.97, per 1000 atoms: 0.50 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: 2.82 Conformation dependent library (CDL) restraints added in 693.1 milliseconds 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: 0.80 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: 3.22 Time building geometry restraints manager: 3.29 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.170 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.009 0.001 TRP C 59 HIS 0.003 0.001 HIS K 48 PHE 0.016 0.001 PHE K 60 TYR 0.010 0.001 TYR K 190 ARG 0.005 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.11957 ( 310) hydrogen bonds : angle 6.50171 ( 876) covalent geometry : bond 0.00292 ( 5154) covalent geometry : angle 0.54976 ( 7003) 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 : 0.876 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: 1.5059 time to fit residues: 167.3447 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 : 0.775 ------------------------------------------------------------------------------- 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 56 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.159692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.133168 restraints weight = 22895.372| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.19 r_work: 0.4155 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5155 Z= 0.213 Angle : 0.568 5.304 7003 Z= 0.316 Chirality : 0.042 0.146 837 Planarity : 0.004 0.041 889 Dihedral : 4.499 26.902 737 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.23 % Allowed : 28.33 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 673 helix: 1.16 (0.27), residues: 352 sheet: -0.73 (0.63), residues: 69 loop : -1.63 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 59 HIS 0.005 0.001 HIS K 106 PHE 0.015 0.002 PHE K 274 TYR 0.025 0.002 TYR K 314 ARG 0.004 0.000 ARG K 208 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 310) hydrogen bonds : angle 5.82155 ( 876) covalent geometry : bond 0.00469 ( 5154) covalent geometry : angle 0.56830 ( 7003) Misc. bond : bond 0.00869 ( 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 107 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.872 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 408 ASN cc_start: 0.8460 (m-40) cc_final: 0.8196 (t0) REVERT: C 56 LYS cc_start: 0.8430 (mppt) cc_final: 0.8036 (mmmm) REVERT: P 78 ASP cc_start: 0.7758 (m-30) cc_final: 0.7288 (m-30) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 1.4080 time to fit residues: 153.9547 Evaluate side-chains 90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 75 GLN 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 = 0.4602 r_free = 0.4602 target = 0.159550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.133134 restraints weight = 23024.325| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.17 r_work: 0.4147 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5155 Z= 0.183 Angle : 0.552 5.985 7003 Z= 0.305 Chirality : 0.042 0.136 837 Planarity : 0.004 0.039 889 Dihedral : 4.453 24.498 737 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.44 % Allowed : 26.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.32), residues: 673 helix: 1.21 (0.27), residues: 354 sheet: -0.92 (0.66), residues: 67 loop : -1.70 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 59 HIS 0.008 0.002 HIS K 106 PHE 0.015 0.001 PHE K 274 TYR 0.017 0.002 TYR K 314 ARG 0.008 0.000 ARG K 208 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 310) hydrogen bonds : angle 5.52197 ( 876) covalent geometry : bond 0.00404 ( 5154) covalent geometry : angle 0.55191 ( 7003) Misc. bond : bond 0.00694 ( 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 112 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.846 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: 0.8491 (m-40) cc_final: 0.8192 (t0) REVERT: B 524 MET cc_start: 0.6707 (ttt) cc_final: 0.6486 (ttt) REVERT: C 56 LYS cc_start: 0.8335 (mppt) cc_final: 0.7897 (mmmm) REVERT: P 78 ASP cc_start: 0.7859 (m-30) cc_final: 0.7300 (m-30) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 1.3837 time to fit residues: 160.5763 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 : 0.748 ------------------------------------------------------------------------------- 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 241 HIS Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 299 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.163552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.137547 restraints weight = 22471.750| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.14 r_work: 0.4241 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5155 Z= 0.124 Angle : 0.520 4.729 7003 Z= 0.285 Chirality : 0.041 0.146 837 Planarity : 0.004 0.038 889 Dihedral : 4.279 32.813 737 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.59 % Allowed : 27.91 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.33), residues: 673 helix: 1.52 (0.28), residues: 354 sheet: -0.70 (0.66), residues: 66 loop : -1.53 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 59 HIS 0.011 0.002 HIS K 106 PHE 0.012 0.001 PHE K 274 TYR 0.014 0.001 TYR K 32 ARG 0.005 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 310) hydrogen bonds : angle 5.23623 ( 876) covalent geometry : bond 0.00272 ( 5154) covalent geometry : angle 0.52040 ( 7003) Misc. bond : bond 0.00433 ( 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 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.782 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 408 ASN cc_start: 0.8489 (m-40) cc_final: 0.8226 (t0) REVERT: C 56 LYS cc_start: 0.8295 (mppt) cc_final: 0.7836 (mmmm) REVERT: K 75 GLN cc_start: 0.5261 (tt0) cc_final: 0.5051 (tp-100) REVERT: K 197 ILE cc_start: 0.8340 (mt) cc_final: 0.8063 (mp) REVERT: P 78 ASP cc_start: 0.7888 (m-30) cc_final: 0.7431 (m-30) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 1.3508 time to fit residues: 148.2030 Evaluate side-chains 96 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain B residue 462 ASP 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 94 SER Chi-restraints excluded: chain K residue 241 HIS Chi-restraints excluded: chain K residue 273 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4678 r_free = 0.4678 target = 0.163690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.137563 restraints weight = 22704.942| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.18 r_work: 0.4239 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2372 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= 0.125 Angle : 0.517 5.336 7003 Z= 0.282 Chirality : 0.041 0.129 837 Planarity : 0.004 0.038 889 Dihedral : 3.971 17.097 735 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.38 % Allowed : 28.54 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.33), residues: 673 helix: 1.60 (0.28), residues: 355 sheet: -0.54 (0.68), residues: 66 loop : -1.45 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 59 HIS 0.012 0.002 HIS K 106 PHE 0.012 0.001 PHE K 274 TYR 0.011 0.001 TYR K 314 ARG 0.004 0.000 ARG K 208 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 310) hydrogen bonds : angle 5.10821 ( 876) covalent geometry : bond 0.00277 ( 5154) covalent geometry : angle 0.51735 ( 7003) Misc. bond : bond 0.00421 ( 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 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASN cc_start: 0.8501 (m-40) cc_final: 0.8220 (t0) REVERT: B 468 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: C 56 LYS cc_start: 0.8268 (mppt) cc_final: 0.7772 (mmmm) REVERT: K 75 GLN cc_start: 0.5260 (tt0) cc_final: 0.4902 (tp-100) REVERT: K 197 ILE cc_start: 0.8358 (mt) cc_final: 0.8102 (mp) REVERT: P 78 ASP cc_start: 0.7822 (m-30) cc_final: 0.7466 (m-30) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 1.5156 time to fit residues: 161.9387 Evaluate side-chains 95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.0370 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.162404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136221 restraints weight = 22843.601| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.16 r_work: 0.4215 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5155 Z= 0.147 Angle : 0.531 5.704 7003 Z= 0.291 Chirality : 0.041 0.137 837 Planarity : 0.004 0.056 889 Dihedral : 4.004 17.186 735 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.17 % Allowed : 28.54 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 673 helix: 1.50 (0.28), residues: 355 sheet: -0.96 (0.62), residues: 76 loop : -1.38 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 517 HIS 0.012 0.001 HIS K 106 PHE 0.013 0.001 PHE K 274 TYR 0.015 0.002 TYR K 32 ARG 0.004 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 310) hydrogen bonds : angle 5.09592 ( 876) covalent geometry : bond 0.00328 ( 5154) covalent geometry : angle 0.53117 ( 7003) Misc. bond : bond 0.00472 ( 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 106 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.806 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: 0.8523 (m-40) cc_final: 0.8235 (t0) REVERT: P 78 ASP cc_start: 0.7770 (m-30) cc_final: 0.7505 (m-30) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 1.4394 time to fit residues: 157.2344 Evaluate side-chains 98 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 94 SER 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 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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 = 0.4672 r_free = 0.4672 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.136728 restraints weight = 22935.956| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.16 r_work: 0.4224 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2664 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= 0.143 Angle : 0.538 6.212 7003 Z= 0.293 Chirality : 0.041 0.146 837 Planarity : 0.004 0.078 889 Dihedral : 4.017 17.166 735 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.38 % Allowed : 29.39 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.33), residues: 673 helix: 1.49 (0.28), residues: 355 sheet: -0.97 (0.63), residues: 76 loop : -1.38 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 517 HIS 0.013 0.001 HIS K 106 PHE 0.033 0.001 PHE C 21 TYR 0.011 0.002 TYR B 464 ARG 0.007 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 310) hydrogen bonds : angle 5.02744 ( 876) covalent geometry : bond 0.00317 ( 5154) covalent geometry : angle 0.53759 ( 7003) Misc. bond : bond 0.00449 ( 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 106 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.764 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: 0.8479 (m-40) cc_final: 0.8187 (t0) REVERT: K 75 GLN cc_start: 0.5333 (tt0) cc_final: 0.4980 (tp-100) REVERT: K 197 ILE cc_start: 0.8335 (mt) cc_final: 0.8103 (mp) REVERT: P 78 ASP cc_start: 0.7718 (m-30) cc_final: 0.7477 (m-30) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 1.4315 time to fit residues: 157.7521 Evaluate side-chains 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 86 VAL 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 Chi-restraints excluded: chain K residue 106 HIS Chi-restraints excluded: chain K residue 273 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.164196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.138357 restraints weight = 22664.686| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.15 r_work: 0.4252 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5155 Z= 0.121 Angle : 0.533 6.062 7003 Z= 0.289 Chirality : 0.041 0.156 837 Planarity : 0.005 0.094 889 Dihedral : 3.923 16.694 735 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.75 % Allowed : 29.81 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.33), residues: 673 helix: 1.54 (0.28), residues: 356 sheet: -0.73 (0.68), residues: 66 loop : -1.39 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 59 HIS 0.013 0.001 HIS K 106 PHE 0.011 0.001 PHE K 274 TYR 0.017 0.001 TYR K 32 ARG 0.009 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 310) hydrogen bonds : angle 4.94013 ( 876) covalent geometry : bond 0.00272 ( 5154) covalent geometry : angle 0.53300 ( 7003) Misc. bond : bond 0.00395 ( 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 101 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASN cc_start: 0.8457 (m-40) cc_final: 0.8185 (t0) REVERT: B 468 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: K 75 GLN cc_start: 0.5219 (tt0) cc_final: 0.4946 (tp-100) REVERT: K 197 ILE cc_start: 0.8366 (mt) cc_final: 0.8149 (mp) outliers start: 13 outliers final: 7 residues processed: 99 average time/residue: 1.3803 time to fit residues: 147.7049 Evaluate side-chains 92 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.165267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.139285 restraints weight = 22408.079| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.15 r_work: 0.4267 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3001 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= 0.113 Angle : 0.530 5.695 7003 Z= 0.288 Chirality : 0.041 0.149 837 Planarity : 0.005 0.095 889 Dihedral : 3.838 16.463 735 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 30.44 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.33), residues: 673 helix: 1.63 (0.27), residues: 357 sheet: -0.76 (0.68), residues: 66 loop : -1.34 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 302 HIS 0.010 0.001 HIS K 106 PHE 0.029 0.001 PHE C 21 TYR 0.011 0.001 TYR K 314 ARG 0.009 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 310) hydrogen bonds : angle 4.81413 ( 876) covalent geometry : bond 0.00254 ( 5154) covalent geometry : angle 0.53039 ( 7003) Misc. bond : bond 0.00363 ( 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 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.832 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 408 ASN cc_start: 0.8369 (m-40) cc_final: 0.8118 (t0) REVERT: B 468 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: K 60 PHE cc_start: 0.5499 (m-10) cc_final: 0.5291 (m-10) REVERT: K 75 GLN cc_start: 0.5164 (tt0) cc_final: 0.4954 (tp-100) REVERT: K 197 ILE cc_start: 0.8390 (mt) cc_final: 0.8190 (mp) REVERT: P 78 ASP cc_start: 0.7735 (m-30) cc_final: 0.7436 (m-30) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 1.3385 time to fit residues: 145.9830 Evaluate side-chains 95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 K residue 2 ILE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 273 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.164366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.138583 restraints weight = 22472.672| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 3.14 r_work: 0.4250 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5155 Z= 0.128 Angle : 0.546 5.633 7003 Z= 0.296 Chirality : 0.041 0.143 837 Planarity : 0.005 0.099 889 Dihedral : 3.848 16.580 735 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.33), residues: 673 helix: 1.59 (0.27), residues: 359 sheet: -0.88 (0.67), residues: 66 loop : -1.33 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 302 HIS 0.010 0.001 HIS K 106 PHE 0.014 0.001 PHE P 43 TYR 0.020 0.002 TYR K 32 ARG 0.010 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 310) hydrogen bonds : angle 4.80973 ( 876) covalent geometry : bond 0.00289 ( 5154) covalent geometry : angle 0.54562 ( 7003) 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 : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASN cc_start: 0.8369 (m-40) cc_final: 0.8115 (t0) REVERT: C 120 ARG cc_start: 0.8988 (tmt-80) cc_final: 0.8755 (tpm170) REVERT: C 144 LEU cc_start: 0.7746 (mp) cc_final: 0.7404 (mt) REVERT: K 75 GLN cc_start: 0.5278 (tt0) cc_final: 0.4892 (tp-100) REVERT: K 127 TYR cc_start: 0.7735 (t80) cc_final: 0.7176 (t80) REVERT: P 78 ASP cc_start: 0.7701 (m-30) cc_final: 0.7370 (m-30) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 1.3477 time to fit residues: 139.3126 Evaluate side-chains 95 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain K residue 273 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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 = 0.4632 r_free = 0.4632 target = 0.159773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.133812 restraints weight = 23043.452| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.13 r_work: 0.4181 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5155 Z= 0.204 Angle : 0.596 6.314 7003 Z= 0.328 Chirality : 0.043 0.141 837 Planarity : 0.005 0.076 889 Dihedral : 4.160 17.557 735 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.33 % Allowed : 31.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 673 helix: 1.12 (0.27), residues: 363 sheet: -1.12 (0.66), residues: 66 loop : -1.63 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 517 HIS 0.010 0.002 HIS K 106 PHE 0.026 0.002 PHE C 21 TYR 0.018 0.002 TYR K 190 ARG 0.007 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 310) hydrogen bonds : angle 5.12971 ( 876) covalent geometry : bond 0.00460 ( 5154) covalent geometry : angle 0.59552 ( 7003) Misc. bond : bond 0.00553 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6875.09 seconds wall clock time: 118 minutes 10.53 seconds (7090.53 seconds total)