Starting phenix.real_space_refine on Mon May 19 03:17:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443.map" model { file = "/net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up5_42443/05_2025/8up5_42443_neut.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.047 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 6767 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: 6 Type Number sf(0) Gaussians P 73 5.49 5 S 22 5.16 5 C 4076 2.51 5 N 1180 2.21 5 O 1459 1.98 5 H 5818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 12628 Number of models: 1 Model: "" Number of chains: 5 Chain: "T" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 2326 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 60} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2614 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 118 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': 8} Unresolved non-hydrogen planarities: 84 Chain: "K" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4658 Classifications: {'peptide': 321} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 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: "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: "P" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1076 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 6.57, per 1000 atoms: 0.52 Number of scatterers: 12628 At special positions: 0 Unit cell: (67.98, 89.61, 131.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 73 15.00 O 1459 8.00 N 1180 7.00 C 4076 6.00 H 5818 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: 3.36 Conformation dependent library (CDL) restraints added in 962.4 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 54.6% alpha, 13.9% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'B' and resid 369 through 394 removed outlier: 4.426A pdb=" N LYS B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.475A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.751A pdb=" N TYR B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.928A pdb=" N LYS B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.542A pdb=" N VAL B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 removed outlier: 3.720A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'K' and resid 43 through 63 Proline residue: K 53 - end of helix 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 182 removed outlier: 3.586A pdb=" N LYS K 181 " --> pdb=" O GLU K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 212 removed outlier: 4.333A 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 271 Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.306A pdb=" N GLY K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 removed outlier: 3.996A pdb=" N ILE K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.940A pdb=" N ASN C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.651A pdb=" N VAL C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 4.272A 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 112 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'P' and resid 16 through 33 removed outlier: 3.925A pdb=" N TYR P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 80 removed outlier: 3.796A pdb=" N ILE P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 361 removed outlier: 3.816A pdb=" N ASP B 403 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420 removed outlier: 3.523A pdb=" N LYS B 419 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AA4, first strand: chain 'K' and resid 23 through 31 removed outlier: 5.765A pdb=" N VAL K 24 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR K 19 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE K 2 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA K 72 " --> pdb=" O ILE K 2 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU K 4 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER K 74 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU K 6 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLY K 76 " --> pdb=" O LEU K 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 142 through 148 removed outlier: 4.934A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL K 139 " --> pdb=" O TYR K 143 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL K 145 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA K 137 " --> pdb=" O VAL K 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY K 147 " --> pdb=" O VAL K 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.102A pdb=" N GLY C 84 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 13 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 8 through 13 321 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 4.03 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: 5757 1.03 - 1.23: 82 1.23 - 1.42: 3063 1.42 - 1.61: 3954 1.61 - 1.81: 39 Bond restraints: 12895 Sorted by residual: bond pdb=" N ASP B 467 " pdb=" H ASP B 467 " ideal model delta sigma weight residual 0.860 1.185 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" N SER K 129 " pdb=" H SER K 129 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" N ILE B 466 " pdb=" H ILE B 466 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N GLY K 131 " pdb=" H GLY K 131 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" N GLY K 130 " pdb=" H GLY K 130 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.68e+01 ... (remaining 12890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 22915 2.45 - 4.91: 278 4.91 - 7.36: 26 7.36 - 9.81: 8 9.81 - 12.27: 4 Bond angle restraints: 23231 Sorted by residual: angle pdb=" N ARG B 530 " pdb=" CA ARG B 530 " pdb=" C ARG B 530 " ideal model delta sigma weight residual 111.11 122.56 -11.45 1.20e+00 6.94e-01 9.11e+01 angle pdb=" N ARG B 532 " pdb=" CA ARG B 532 " pdb=" C ARG B 532 " ideal model delta sigma weight residual 110.50 121.45 -10.95 1.41e+00 5.03e-01 6.03e+01 angle pdb=" O3' U T 36 " pdb=" C3' U T 36 " pdb=" C2' U T 36 " ideal model delta sigma weight residual 109.50 119.65 -10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" CA THR K 133 " pdb=" C THR K 133 " pdb=" O THR K 133 " ideal model delta sigma weight residual 120.36 113.28 7.08 1.07e+00 8.73e-01 4.37e+01 angle pdb=" N ARG B 532 " pdb=" CA ARG B 532 " pdb=" CB ARG B 532 " ideal model delta sigma weight residual 110.17 101.93 8.24 1.44e+00 4.82e-01 3.28e+01 ... (remaining 23226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 5771 33.82 - 67.63: 403 67.63 - 101.45: 48 101.45 - 135.26: 3 135.26 - 169.08: 2 Dihedral angle restraints: 6227 sinusoidal: 3872 harmonic: 2355 Sorted by residual: dihedral pdb=" C ILE B 466 " pdb=" N ILE B 466 " pdb=" CA ILE B 466 " pdb=" CB ILE B 466 " ideal model delta harmonic sigma weight residual -122.00 -136.47 14.47 0 2.50e+00 1.60e-01 3.35e+01 dihedral pdb=" O4' C T 74 " pdb=" C1' C T 74 " pdb=" N1 C T 74 " pdb=" C2 C T 74 " ideal model delta sinusoidal sigma weight residual -128.00 -42.70 -85.30 1 1.70e+01 3.46e-03 3.05e+01 dihedral pdb=" C4' C T 74 " pdb=" C3' C T 74 " pdb=" O3' C T 74 " pdb=" P C T 75 " ideal model delta sinusoidal sigma weight residual -110.00 59.08 -169.08 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1170 0.096 - 0.191: 53 0.191 - 0.287: 3 0.287 - 0.382: 1 0.382 - 0.478: 5 Chirality restraints: 1232 Sorted by residual: chirality pdb=" P U T 36 " pdb=" OP1 U T 36 " pdb=" OP2 U T 36 " pdb=" O5' U T 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" P C T 75 " pdb=" OP1 C T 75 " pdb=" OP2 C T 75 " pdb=" O5' C T 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" P C T 74 " pdb=" OP1 C T 74 " pdb=" OP2 C T 74 " pdb=" O5' C T 74 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 1229 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 132 " -0.234 2.00e-02 2.50e+03 3.94e-01 2.33e+03 pdb=" CG ASN K 132 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN K 132 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN K 132 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN K 132 " 0.632 2.00e-02 2.50e+03 pdb="HD22 ASN K 132 " -0.653 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 466 " -0.095 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" N ASP B 467 " 0.262 2.00e-02 2.50e+03 pdb=" CA ASP B 467 " -0.076 2.00e-02 2.50e+03 pdb=" H ASP B 467 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 530 " 0.051 2.00e-02 2.50e+03 8.94e-02 7.98e+01 pdb=" N ALA B 531 " -0.154 2.00e-02 2.50e+03 pdb=" CA ALA B 531 " 0.042 2.00e-02 2.50e+03 pdb=" H ALA B 531 " 0.061 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 27 1.64 - 2.38: 5087 2.38 - 3.12: 38487 3.12 - 3.86: 53813 3.86 - 4.60: 84024 Warning: very small nonbonded interaction distances. Nonbonded interactions: 181438 Sorted by model distance: nonbonded pdb="HD22 ASN K 105 " pdb=" CD2 TYR K 314 " model vdw 0.903 2.240 nonbonded pdb=" OH TYR K 314 " pdb=" CG2 VAL K 319 " model vdw 1.114 3.100 nonbonded pdb="HH21 ARG B 532 " pdb=" HB2 PRO K 77 " model vdw 1.126 2.270 nonbonded pdb=" CG ASN K 105 " pdb=" HE2 TYR K 314 " model vdw 1.127 2.200 nonbonded pdb=" HH TYR K 314 " pdb="HG21 VAL K 319 " model vdw 1.171 2.270 ... (remaining 181433 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 36.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 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 : 0.006 0.378 7078 Z= 0.501 Angle : 0.713 11.452 9951 Z= 0.452 Chirality : 0.051 0.478 1232 Planarity : 0.004 0.052 991 Dihedral : 21.347 169.079 3023 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.60 % Allowed : 26.65 % Favored : 72.75 % Cbeta Deviations : 0.15 % 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: 0.41 (0.33), residues: 694 helix: 1.36 (0.29), residues: 349 sheet: 0.05 (0.59), residues: 78 loop : -1.11 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 302 HIS 0.006 0.001 HIS K 106 PHE 0.008 0.001 PHE C 27 TYR 0.016 0.001 TYR P 36 ARG 0.003 0.000 ARG P 38 Details of bonding type rmsd hydrogen bonds : bond 0.14562 ( 372) hydrogen bonds : angle 6.72820 ( 995) covalent geometry : bond 0.00377 ( 7077) covalent geometry : angle 0.71348 ( 9951) Misc. bond : bond 0.37800 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.819 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 outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.3947 time to fit residues: 46.2778 Evaluate side-chains 84 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 ASN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 ASN C 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.161545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.123368 restraints weight = 31676.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.128310 restraints weight = 16682.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.131538 restraints weight = 10603.572| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7078 Z= 0.143 Angle : 0.516 3.918 9951 Z= 0.285 Chirality : 0.038 0.151 1232 Planarity : 0.004 0.036 991 Dihedral : 21.587 168.782 1924 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.20 % Allowed : 25.65 % Favored : 72.14 % 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 (0.32), residues: 694 helix: 1.49 (0.28), residues: 351 sheet: -0.19 (0.57), residues: 77 loop : -1.19 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 291 HIS 0.007 0.002 HIS K 48 PHE 0.011 0.001 PHE B 506 TYR 0.020 0.002 TYR K 314 ARG 0.003 0.001 ARG B 532 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 372) hydrogen bonds : angle 5.32421 ( 995) covalent geometry : bond 0.00304 ( 7077) covalent geometry : angle 0.51602 ( 9951) Misc. bond : bond 0.00390 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.834 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: symmetry clash REVERT: C 65 ARG cc_start: 0.4676 (mmt180) cc_final: 0.4399 (mmt90) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.3694 time to fit residues: 51.7226 Evaluate side-chains 92 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.156303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117920 restraints weight = 32772.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122566 restraints weight = 17773.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.125662 restraints weight = 11559.216| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7078 Z= 0.230 Angle : 0.564 4.519 9951 Z= 0.317 Chirality : 0.039 0.142 1232 Planarity : 0.004 0.042 991 Dihedral : 21.604 168.292 1922 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.01 % Allowed : 26.05 % Favored : 69.94 % 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: -0.41 (0.31), residues: 694 helix: 0.84 (0.27), residues: 351 sheet: -0.48 (0.56), residues: 77 loop : -1.70 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 291 HIS 0.004 0.002 HIS K 48 PHE 0.018 0.002 PHE B 468 TYR 0.022 0.002 TYR K 190 ARG 0.003 0.001 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.06161 ( 372) hydrogen bonds : angle 5.42360 ( 995) covalent geometry : bond 0.00503 ( 7077) covalent geometry : angle 0.56419 ( 9951) Misc. bond : bond 0.00454 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.841 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 outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 0.3521 time to fit residues: 46.4329 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 262 MET Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.158927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.120668 restraints weight = 32331.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.125505 restraints weight = 17162.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.128739 restraints weight = 11020.007| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7078 Z= 0.145 Angle : 0.501 3.736 9951 Z= 0.278 Chirality : 0.038 0.141 1232 Planarity : 0.004 0.034 991 Dihedral : 21.568 171.029 1922 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.61 % Allowed : 25.85 % Favored : 70.54 % 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: -0.08 (0.32), residues: 694 helix: 1.11 (0.27), residues: 351 sheet: -0.82 (0.55), residues: 82 loop : -1.38 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 302 HIS 0.006 0.002 HIS K 48 PHE 0.010 0.001 PHE B 468 TYR 0.017 0.002 TYR K 314 ARG 0.003 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 372) hydrogen bonds : angle 5.05531 ( 995) covalent geometry : bond 0.00310 ( 7077) covalent geometry : angle 0.50140 ( 9951) Misc. bond : bond 0.00520 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.851 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: K 135 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6838 (p) outliers start: 18 outliers final: 14 residues processed: 99 average time/residue: 0.3240 time to fit residues: 44.9036 Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.158149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.119826 restraints weight = 32593.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124638 restraints weight = 17354.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.127845 restraints weight = 11172.334| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7078 Z= 0.158 Angle : 0.511 4.502 9951 Z= 0.282 Chirality : 0.038 0.141 1232 Planarity : 0.004 0.033 991 Dihedral : 21.524 170.481 1922 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.81 % Allowed : 26.45 % Favored : 69.74 % 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: 694 helix: 1.09 (0.27), residues: 351 sheet: -0.86 (0.55), residues: 82 loop : -1.40 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 291 HIS 0.006 0.002 HIS K 106 PHE 0.011 0.001 PHE B 468 TYR 0.017 0.002 TYR K 314 ARG 0.002 0.000 ARG P 38 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 372) hydrogen bonds : angle 5.02402 ( 995) covalent geometry : bond 0.00346 ( 7077) covalent geometry : angle 0.51085 ( 9951) Misc. bond : bond 0.00541 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.797 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: K 135 VAL cc_start: 0.7105 (OUTLIER) cc_final: 0.6854 (p) outliers start: 19 outliers final: 16 residues processed: 94 average time/residue: 0.3088 time to fit residues: 40.9299 Evaluate side-chains 97 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4530 r_free = 0.4530 target = 0.158586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.120330 restraints weight = 32813.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.125186 restraints weight = 17293.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.128421 restraints weight = 11048.429| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7078 Z= 0.141 Angle : 0.498 4.366 9951 Z= 0.276 Chirality : 0.038 0.140 1232 Planarity : 0.004 0.032 991 Dihedral : 21.483 170.942 1922 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.21 % Allowed : 26.25 % Favored : 69.54 % 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: -0.04 (0.32), residues: 694 helix: 1.10 (0.27), residues: 352 sheet: -0.80 (0.55), residues: 82 loop : -1.29 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 302 HIS 0.007 0.002 HIS K 106 PHE 0.010 0.001 PHE B 468 TYR 0.017 0.002 TYR K 314 ARG 0.003 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 372) hydrogen bonds : angle 4.93170 ( 995) covalent geometry : bond 0.00307 ( 7077) covalent geometry : angle 0.49768 ( 9951) Misc. bond : bond 0.00558 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 THR cc_start: 0.6603 (m) cc_final: 0.6355 (m) REVERT: K 135 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6823 (p) REVERT: K 233 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: C 60 MET cc_start: 0.4905 (ttm) cc_final: 0.4599 (tmm) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.3422 time to fit residues: 47.0081 Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 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 = 0.4583 r_free = 0.4583 target = 0.161599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.123541 restraints weight = 33456.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.128470 restraints weight = 17513.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.131702 restraints weight = 11258.293| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7078 Z= 0.127 Angle : 0.492 4.726 9951 Z= 0.271 Chirality : 0.037 0.140 1232 Planarity : 0.003 0.031 991 Dihedral : 21.430 171.019 1922 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.61 % Allowed : 26.05 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.32), residues: 694 helix: 1.25 (0.28), residues: 353 sheet: -0.74 (0.55), residues: 82 loop : -1.18 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 302 HIS 0.006 0.001 HIS K 106 PHE 0.010 0.001 PHE B 468 TYR 0.017 0.002 TYR K 314 ARG 0.003 0.000 ARG B 532 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 372) hydrogen bonds : angle 4.83970 ( 995) covalent geometry : bond 0.00276 ( 7077) covalent geometry : angle 0.49248 ( 9951) Misc. bond : bond 0.00553 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 THR cc_start: 0.6477 (m) cc_final: 0.6226 (m) REVERT: K 135 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6818 (p) REVERT: K 233 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6012 (tt0) REVERT: C 60 MET cc_start: 0.4920 (ttm) cc_final: 0.4627 (tmm) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.3222 time to fit residues: 45.3762 Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.162279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.124038 restraints weight = 33557.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.129031 restraints weight = 17330.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.132301 restraints weight = 11030.941| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7078 Z= 0.116 Angle : 0.483 4.812 9951 Z= 0.265 Chirality : 0.037 0.141 1232 Planarity : 0.003 0.030 991 Dihedral : 21.351 171.185 1922 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.61 % Allowed : 26.65 % Favored : 69.74 % 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 (0.32), residues: 694 helix: 1.37 (0.28), residues: 354 sheet: -0.25 (0.56), residues: 77 loop : -1.04 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 302 HIS 0.007 0.001 HIS K 106 PHE 0.010 0.001 PHE B 468 TYR 0.021 0.002 TYR P 36 ARG 0.002 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 372) hydrogen bonds : angle 4.75819 ( 995) covalent geometry : bond 0.00251 ( 7077) covalent geometry : angle 0.48309 ( 9951) Misc. bond : bond 0.00554 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 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: K 51 THR cc_start: 0.6484 (m) cc_final: 0.6225 (m) REVERT: K 135 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.6722 (p) REVERT: K 233 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5979 (tt0) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.3206 time to fit residues: 42.1615 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN K 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.159333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.121286 restraints weight = 32395.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.126115 restraints weight = 17149.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.129293 restraints weight = 11001.912| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7078 Z= 0.133 Angle : 0.497 4.570 9951 Z= 0.272 Chirality : 0.037 0.140 1232 Planarity : 0.003 0.030 991 Dihedral : 21.339 171.155 1922 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.21 % Allowed : 26.25 % Favored : 69.54 % 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: 0.36 (0.32), residues: 694 helix: 1.32 (0.28), residues: 354 sheet: -0.32 (0.56), residues: 77 loop : -1.05 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 302 HIS 0.005 0.001 HIS K 48 PHE 0.010 0.001 PHE B 468 TYR 0.021 0.002 TYR K 127 ARG 0.003 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 372) hydrogen bonds : angle 4.80133 ( 995) covalent geometry : bond 0.00291 ( 7077) covalent geometry : angle 0.49717 ( 9951) Misc. bond : bond 0.00536 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 THR cc_start: 0.6521 (m) cc_final: 0.6253 (m) REVERT: K 135 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6758 (p) REVERT: K 233 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6100 (tt0) outliers start: 21 outliers final: 16 residues processed: 92 average time/residue: 0.3203 time to fit residues: 41.7071 Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 256 ASN Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.159111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121525 restraints weight = 31940.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.126227 restraints weight = 16829.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.129345 restraints weight = 10739.397| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 7078 Z= 0.223 Angle : 0.894 58.691 9951 Z= 0.559 Chirality : 0.037 0.143 1232 Planarity : 0.004 0.043 991 Dihedral : 21.339 171.161 1922 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.81 % Allowed : 26.85 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.32), residues: 694 helix: 1.30 (0.28), residues: 354 sheet: -0.31 (0.56), residues: 77 loop : -1.03 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 291 HIS 0.005 0.001 HIS K 106 PHE 0.010 0.001 PHE B 468 TYR 0.017 0.002 TYR K 127 ARG 0.002 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 372) hydrogen bonds : angle 4.80153 ( 995) covalent geometry : bond 0.00455 ( 7077) covalent geometry : angle 0.89440 ( 9951) Misc. bond : bond 0.00535 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 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 ILE 465 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 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 36 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 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 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 ILE 10 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 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 SER 68 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 THR cc_start: 0.6537 (m) cc_final: 0.6268 (m) REVERT: K 135 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6758 (p) REVERT: K 233 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6103 (tt0) outliers start: 19 outliers final: 17 residues processed: 89 average time/residue: 0.3296 time to fit residues: 41.5622 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.159111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121453 restraints weight = 32171.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.126155 restraints weight = 16896.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.129347 restraints weight = 10748.093| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 7078 Z= 0.223 Angle : 0.894 58.723 9951 Z= 0.559 Chirality : 0.037 0.143 1232 Planarity : 0.004 0.043 991 Dihedral : 21.339 171.161 1922 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.81 % Allowed : 26.85 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.32), residues: 694 helix: 1.30 (0.28), residues: 354 sheet: -0.31 (0.56), residues: 77 loop : -1.03 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 291 HIS 0.005 0.001 HIS K 106 PHE 0.010 0.001 PHE B 468 TYR 0.017 0.002 TYR K 127 ARG 0.002 0.000 ARG K 84 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 372) hydrogen bonds : angle 4.80152 ( 995) covalent geometry : bond 0.00454 ( 7077) covalent geometry : angle 0.89443 ( 9951) Misc. bond : bond 0.00535 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.56 seconds wall clock time: 81 minutes 55.83 seconds (4915.83 seconds total)