Starting phenix.real_space_refine on Mon Apr 8 21:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/04_2024/8tb7_41145_trim_updated.pdb" } resolution = 2.94 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= -0.001 sd= 0.061 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 1082 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 S 33 5.16 5 C 4348 2.51 5 N 1130 2.21 5 O 1279 1.98 5 F 2 1.80 5 H 6676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13468 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5213 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3275 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1746 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3197 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'ZOB': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 6.02, per 1000 atoms: 0.45 Number of scatterers: 13468 At special positions: 0 Unit cell: (74.34, 128.62, 107.38, 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 33 16.00 F 2 9.00 O 1279 8.00 N 1130 7.00 C 4348 6.00 H 6676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 380 " - pdb=" SG CYS R 414 " distance=2.02 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 11 sheets defined 31.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'R' and resid 55 through 77 removed outlier: 3.621A pdb=" N VAL R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 107 removed outlier: 4.118A pdb=" N MET R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Proline residue: R 104 - end of helix Processing helix chain 'R' and resid 122 through 154 removed outlier: 4.009A pdb=" N LEU R 126 " --> pdb=" O VAL R 122 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU R 128 " --> pdb=" O CYS R 124 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE R 129 " --> pdb=" O ARG R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 187 Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 217 through 265 Proline residue: R 229 - end of helix removed outlier: 4.464A pdb=" N ILE R 233 " --> pdb=" O PRO R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 287 removed outlier: 3.881A pdb=" N LYS R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 279 " --> pdb=" O ASP R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 325 removed outlier: 3.750A pdb=" N ASP R 307 " --> pdb=" O PRO R 303 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE R 308 " --> pdb=" O GLU R 304 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG R 309 " --> pdb=" O MET R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 348 Processing helix chain 'R' and resid 366 through 391 removed outlier: 4.595A pdb=" N CYS R 380 " --> pdb=" O GLN R 376 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 404 through 423 removed outlier: 3.932A pdb=" N PHE R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR R 416 " --> pdb=" O TYR R 412 " (cutoff:3.500A) Proline residue: R 419 - end of helix Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 108 through 111 No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 185 through 188 No H-bonds generated for 'chain 'L' and resid 185 through 188' Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 121 through 123 removed outlier: 3.556A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.014A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 164 through 168 removed outlier: 4.550A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 225 " --> pdb=" O TYR H 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.838A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA N 23 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU N 20 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.958A pdb=" N ARG N 38 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= H, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.549A pdb=" N LYS L 105 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 86 through 88 removed outlier: 5.939A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.919A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 147 through 152 322 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6670 1.04 - 1.23: 484 1.23 - 1.43: 2549 1.43 - 1.63: 3868 1.63 - 1.83: 48 Bond restraints: 13619 Sorted by residual: bond pdb=" ND2 ASN R 426 " pdb="HD21 ASN R 426 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN R 426 " pdb="HD22 ASN R 426 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C21 ZOB R 601 " pdb=" N26 ZOB R 601 " ideal model delta sigma weight residual 1.451 1.361 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" CA ASN R 426 " pdb=" C ASN R 426 " ideal model delta sigma weight residual 1.524 1.467 0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" N10 ZOB R 601 " pdb=" S15 ZOB R 601 " ideal model delta sigma weight residual 1.717 1.648 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 13614 not shown) Histogram of bond angle deviations from ideal: 72.43 - 84.76: 12 84.76 - 97.10: 0 97.10 - 109.43: 8878 109.43 - 121.76: 13121 121.76 - 134.09: 2510 Bond angle restraints: 24521 Sorted by residual: angle pdb=" C ALA N 40 " pdb=" CA ALA N 40 " pdb=" HA ALA N 40 " ideal model delta sigma weight residual 109.00 72.43 36.57 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C GLN R 402 " pdb=" CA GLN R 402 " pdb=" HA GLN R 402 " ideal model delta sigma weight residual 109.00 73.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB LEU R 234 " pdb=" CA LEU R 234 " pdb=" HA LEU R 234 " ideal model delta sigma weight residual 109.00 73.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N GLN R 402 " pdb=" CA GLN R 402 " pdb=" HA GLN R 402 " ideal model delta sigma weight residual 110.00 74.91 35.09 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C CYS R 124 " pdb=" CA CYS R 124 " pdb=" HA CYS R 124 " ideal model delta sigma weight residual 109.00 74.13 34.87 3.00e+00 1.11e-01 1.35e+02 ... (remaining 24516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 6333 34.39 - 68.78: 144 68.78 - 103.17: 7 103.17 - 137.57: 0 137.57 - 171.96: 1 Dihedral angle restraints: 6485 sinusoidal: 3436 harmonic: 3049 Sorted by residual: dihedral pdb=" CA ILE L 76 " pdb=" C ILE L 76 " pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA GLU H 162 " pdb=" C GLU H 162 " pdb=" N PRO H 163 " pdb=" CA PRO H 163 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" C18 ZOB R 601 " pdb=" N10 ZOB R 601 " pdb=" S15 ZOB R 601 " pdb=" C8 ZOB R 601 " ideal model delta sinusoidal sigma weight residual -138.69 33.27 -171.96 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 6482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1004 0.090 - 0.179: 62 0.179 - 0.269: 1 0.269 - 0.358: 1 0.358 - 0.448: 3 Chirality restraints: 1071 Sorted by residual: chirality pdb=" CA GLN R 402 " pdb=" N GLN R 402 " pdb=" C GLN R 402 " pdb=" CB GLN R 402 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ALA N 40 " pdb=" N ALA N 40 " pdb=" C ALA N 40 " pdb=" CB ALA N 40 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA CYS R 124 " pdb=" N CYS R 124 " pdb=" C CYS R 124 " pdb=" CB CYS R 124 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1068 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 426 " -0.053 2.00e-02 2.50e+03 5.11e-02 3.91e+01 pdb=" CG ASN R 426 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN R 426 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN R 426 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN R 426 " 0.072 2.00e-02 2.50e+03 pdb="HD22 ASN R 426 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 382 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO R 383 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 383 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 383 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C27 ZOB R 601 " 0.022 2.00e-02 2.50e+03 1.22e-02 3.35e+00 pdb=" C28 ZOB R 601 " 0.002 2.00e-02 2.50e+03 pdb=" C29 ZOB R 601 " 0.000 2.00e-02 2.50e+03 pdb=" C30 ZOB R 601 " 0.007 2.00e-02 2.50e+03 pdb=" C32 ZOB R 601 " 0.000 2.00e-02 2.50e+03 pdb=" C33 ZOB R 601 " -0.002 2.00e-02 2.50e+03 pdb=" F34 ZOB R 601 " -0.017 2.00e-02 2.50e+03 pdb=" F35 ZOB R 601 " -0.021 2.00e-02 2.50e+03 pdb=" N31 ZOB R 601 " 0.008 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 288 2.13 - 2.75: 24167 2.75 - 3.36: 35784 3.36 - 3.98: 46193 3.98 - 4.60: 72566 Nonbonded interactions: 178998 Sorted by model distance: nonbonded pdb=" O TRP R 254 " pdb="HD21 ASN R 258 " model vdw 1.512 1.850 nonbonded pdb="HE22 GLN H 85 " pdb=" OD1 ASN H 87 " model vdw 1.561 1.850 nonbonded pdb="HD22 ASN R 69 " pdb=" OD2 ASP R 95 " model vdw 1.593 1.850 nonbonded pdb=" HA CYS R 124 " pdb=" HB3 CYS R 124 " model vdw 1.624 1.952 nonbonded pdb=" HA LEU R 234 " pdb=" HB2 LEU R 234 " model vdw 1.641 1.952 ... (remaining 178993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.190 Extract box with map and model: 4.010 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 46.390 Find NCS groups from input model: 0.250 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 6943 Z= 0.274 Angle : 0.706 18.863 9435 Z= 0.343 Chirality : 0.048 0.448 1071 Planarity : 0.004 0.052 1185 Dihedral : 13.760 171.957 2443 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.07 (0.30), residues: 859 helix: 1.93 (0.33), residues: 254 sheet: 0.25 (0.34), residues: 260 loop : -1.59 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 PHE 0.013 0.001 PHE N 47 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG N 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 2.6584 time to fit residues: 376.8901 Evaluate side-chains 104 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6943 Z= 0.194 Angle : 0.568 10.474 9435 Z= 0.293 Chirality : 0.047 0.448 1071 Planarity : 0.004 0.051 1185 Dihedral : 7.699 170.044 956 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.77 % Allowed : 9.40 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 859 helix: 2.05 (0.32), residues: 256 sheet: 0.30 (0.34), residues: 260 loop : -1.60 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 176 HIS 0.003 0.001 HIS L 200 PHE 0.012 0.001 PHE N 47 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7200 (tt) REVERT: H 22 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7724 (ttm-80) REVERT: L 149 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7611 (mp10) outliers start: 13 outliers final: 2 residues processed: 110 average time/residue: 2.5290 time to fit residues: 293.3235 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 160 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6943 Z= 0.260 Angle : 0.587 10.711 9435 Z= 0.306 Chirality : 0.048 0.447 1071 Planarity : 0.004 0.052 1185 Dihedral : 7.722 170.633 956 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 2.18 % Allowed : 10.22 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.29), residues: 859 helix: 2.00 (0.32), residues: 258 sheet: 0.21 (0.34), residues: 258 loop : -1.72 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 176 HIS 0.005 0.001 HIS L 200 PHE 0.017 0.002 PHE N 47 TYR 0.013 0.001 TYR L 92 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7126 (tt) REVERT: H 22 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7637 (ttm-80) REVERT: H 162 GLU cc_start: 0.7952 (tt0) cc_final: 0.7704 (tt0) REVERT: H 226 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7353 (mm-30) REVERT: L 82 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7104 (pm20) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 2.4949 time to fit residues: 305.3972 Evaluate side-chains 110 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 163 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 157 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6943 Z= 0.179 Angle : 0.546 10.538 9435 Z= 0.283 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.048 1185 Dihedral : 7.663 171.443 956 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.32 % Allowed : 11.31 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.24 (0.30), residues: 859 helix: 2.21 (0.32), residues: 258 sheet: 0.30 (0.34), residues: 258 loop : -1.62 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.011 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7114 (tt) REVERT: R 226 PHE cc_start: 0.5484 (m-10) cc_final: 0.5116 (m-10) REVERT: H 22 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7655 (ttm-80) REVERT: L 82 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7061 (pm20) outliers start: 17 outliers final: 7 residues processed: 113 average time/residue: 2.4388 time to fit residues: 291.4214 Evaluate side-chains 111 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6943 Z= 0.206 Angle : 0.556 10.568 9435 Z= 0.290 Chirality : 0.048 0.444 1071 Planarity : 0.004 0.058 1185 Dihedral : 7.675 171.308 956 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.91 % Allowed : 12.40 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.24 (0.29), residues: 859 helix: 2.20 (0.32), residues: 256 sheet: 0.31 (0.34), residues: 258 loop : -1.59 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.012 0.001 PHE N 47 TYR 0.011 0.001 TYR L 92 ARG 0.001 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7115 (tt) REVERT: R 226 PHE cc_start: 0.5553 (m-10) cc_final: 0.5160 (m-10) REVERT: R 244 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7279 (tpm-80) REVERT: H 22 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7660 (ttm-80) REVERT: L 82 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7047 (pm20) outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 2.4741 time to fit residues: 284.9593 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6943 Z= 0.188 Angle : 0.543 10.541 9435 Z= 0.282 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.056 1185 Dihedral : 7.623 171.376 956 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.63 % Allowed : 14.03 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.34 (0.30), residues: 859 helix: 2.28 (0.32), residues: 256 sheet: 0.39 (0.34), residues: 260 loop : -1.57 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.011 0.001 PHE L 211 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7109 (tt) REVERT: R 226 PHE cc_start: 0.5491 (m-10) cc_final: 0.5037 (m-10) REVERT: H 22 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7679 (ttm-80) outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 2.4654 time to fit residues: 283.8657 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0570 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 157 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6943 Z= 0.175 Angle : 0.531 10.534 9435 Z= 0.275 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.054 1185 Dihedral : 7.566 171.387 956 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 14.71 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 859 helix: 2.34 (0.33), residues: 256 sheet: 0.43 (0.34), residues: 260 loop : -1.53 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.012 0.001 PHE L 211 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7101 (tt) REVERT: R 226 PHE cc_start: 0.5520 (m-10) cc_final: 0.4962 (m-10) REVERT: R 244 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.7332 (tpm-80) REVERT: H 22 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7673 (ttm-80) REVERT: H 226 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7077 (mm-30) REVERT: N 27 ARG cc_start: 0.6486 (ttt180) cc_final: 0.6136 (mtp180) REVERT: N 77 THR cc_start: 0.4413 (OUTLIER) cc_final: 0.4067 (p) REVERT: L 82 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: L 149 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7315 (mp10) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 2.4622 time to fit residues: 288.7787 Evaluate side-chains 110 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6943 Z= 0.191 Angle : 0.539 10.597 9435 Z= 0.279 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.053 1185 Dihedral : 7.568 171.557 956 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.18 % Allowed : 14.85 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.40 (0.30), residues: 859 helix: 2.32 (0.33), residues: 256 sheet: 0.43 (0.34), residues: 260 loop : -1.52 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 176 HIS 0.003 0.001 HIS L 200 PHE 0.010 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7101 (tt) REVERT: R 226 PHE cc_start: 0.5411 (m-10) cc_final: 0.4899 (m-10) REVERT: R 244 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7259 (tpm-80) REVERT: R 286 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7935 (t0) REVERT: H 22 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7651 (ttm-80) REVERT: N 77 THR cc_start: 0.4443 (OUTLIER) cc_final: 0.4081 (p) REVERT: L 82 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6990 (pm20) outliers start: 16 outliers final: 5 residues processed: 108 average time/residue: 2.4999 time to fit residues: 285.7145 Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN L 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6943 Z= 0.160 Angle : 0.525 10.492 9435 Z= 0.270 Chirality : 0.046 0.445 1071 Planarity : 0.004 0.052 1185 Dihedral : 7.501 171.674 956 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.63 % Allowed : 15.12 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.52 (0.30), residues: 859 helix: 2.43 (0.33), residues: 256 sheet: 0.48 (0.34), residues: 260 loop : -1.45 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 176 HIS 0.002 0.001 HIS L 200 PHE 0.012 0.001 PHE L 211 TYR 0.009 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7093 (tt) REVERT: R 226 PHE cc_start: 0.5492 (m-10) cc_final: 0.4955 (m-10) REVERT: R 244 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7319 (tpm-80) REVERT: R 286 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7984 (t0) REVERT: H 22 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7666 (ttm-80) REVERT: L 82 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6977 (pm20) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 2.3536 time to fit residues: 261.2544 Evaluate side-chains 106 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 ASN L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6943 Z= 0.207 Angle : 0.551 10.676 9435 Z= 0.283 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.052 1185 Dihedral : 7.542 171.637 956 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.50 % Allowed : 15.67 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.30), residues: 859 helix: 2.30 (0.33), residues: 256 sheet: 0.41 (0.34), residues: 262 loop : -1.48 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 PHE 0.013 0.001 PHE N 47 TYR 0.010 0.001 TYR L 50 ARG 0.002 0.000 ARG N 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.7641 (tp) cc_final: 0.7300 (tt) REVERT: R 165 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7067 (tt) REVERT: R 226 PHE cc_start: 0.5620 (m-10) cc_final: 0.5080 (m-10) REVERT: R 286 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7989 (t0) REVERT: H 22 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7640 (ttm-80) REVERT: L 82 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6991 (pm20) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 2.5606 time to fit residues: 283.3524 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 ASN L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136130 restraints weight = 21953.284| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.97 r_work: 0.3372 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6943 Z= 0.207 Angle : 0.554 10.650 9435 Z= 0.285 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.051 1185 Dihedral : 7.562 171.784 956 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.50 % Allowed : 15.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.39 (0.30), residues: 859 helix: 2.26 (0.33), residues: 256 sheet: 0.40 (0.34), residues: 262 loop : -1.46 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 176 HIS 0.003 0.001 HIS L 200 PHE 0.012 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.003 0.000 ARG R 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6228.80 seconds wall clock time: 110 minutes 43.16 seconds (6643.16 seconds total)