Starting phenix.real_space_refine on Sun Dec 10 12:47:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_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_41145/12_2023/8tb7_41145_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_41145_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tb7_41145/12_2023/8tb7_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-1.21rc1-5172/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: 6.56, per 1000 atoms: 0.49 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: 10.57 Conformation dependent library (CDL) restraints added in 1.5 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: 2.02 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: 4.70 Time building geometry restraints manager: 10.97 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: 6241 34.39 - 68.78: 96 68.78 - 103.17: 7 103.17 - 137.57: 0 137.57 - 171.96: 1 Dihedral angle restraints: 6345 sinusoidal: 3296 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 6342 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.210 Extract box with map and model: 3.970 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.870 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.870 ------------------------------------------------------------------------------- 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 : 1.069 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: 2.6210 time to fit residues: 371.5796 Evaluate side-chains 104 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3822 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 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: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN H 87 ASN L 102 GLN L 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6943 Z= 0.182 Angle : 0.566 10.493 9435 Z= 0.291 Chirality : 0.047 0.448 1071 Planarity : 0.004 0.051 1185 Dihedral : 7.715 170.576 956 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.77 % Allowed : 8.86 % Favored : 89.37 % 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: 0.19 (0.30), residues: 859 helix: 2.07 (0.33), residues: 256 sheet: 0.31 (0.34), residues: 260 loop : -1.57 (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 0.010 0.001 TYR L 92 ARG 0.001 0.000 ARG L 67 *********************** 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 118 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 109 average time/residue: 2.5473 time to fit residues: 292.2862 Evaluate side-chains 104 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.0021 time to fit residues: 3.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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** L 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1111 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= 0.177 Angle : 0.545 10.476 9435 Z= 0.281 Chirality : 0.047 0.447 1071 Planarity : 0.004 0.050 1185 Dihedral : 7.594 170.266 956 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.36 % Allowed : 10.63 % Favored : 88.01 % 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: 0.28 (0.30), residues: 859 helix: 2.22 (0.33), residues: 256 sheet: 0.33 (0.34), residues: 260 loop : -1.56 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 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 118 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 114 average time/residue: 2.4154 time to fit residues: 291.1185 Evaluate side-chains 103 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.3086 time to fit residues: 1.7501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** L 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1224 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= 0.172 Angle : 0.535 10.511 9435 Z= 0.277 Chirality : 0.047 0.447 1071 Planarity : 0.004 0.048 1185 Dihedral : 7.554 170.906 956 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.91 % Allowed : 10.90 % Favored : 87.19 % 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: 0.36 (0.30), residues: 859 helix: 2.32 (0.33), residues: 258 sheet: 0.34 (0.34), residues: 258 loop : -1.53 (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 0.013 0.001 PHE L 211 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 118 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 113 average time/residue: 2.4599 time to fit residues: 293.7517 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.3662 time to fit residues: 1.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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** L 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6943 Z= 0.169 Angle : 0.532 10.517 9435 Z= 0.274 Chirality : 0.046 0.447 1071 Planarity : 0.004 0.047 1185 Dihedral : 7.519 170.885 956 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.23 % Allowed : 12.53 % Favored : 86.24 % 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: 0.40 (0.30), residues: 859 helix: 2.35 (0.33), residues: 258 sheet: 0.37 (0.34), residues: 258 loop : -1.50 (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 0.014 0.001 PHE L 211 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG R 244 *********************** 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 114 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 2.2682 time to fit residues: 264.1478 Evaluate side-chains 109 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.7034 time to fit residues: 3.8622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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** L 102 GLN L 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6943 Z= 0.187 Angle : 0.540 10.584 9435 Z= 0.280 Chirality : 0.047 0.446 1071 Planarity : 0.004 0.055 1185 Dihedral : 7.573 170.923 956 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.04 % Allowed : 12.81 % Favored : 85.15 % 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: 0.42 (0.30), residues: 859 helix: 2.38 (0.33), residues: 256 sheet: 0.37 (0.34), residues: 258 loop : -1.47 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.015 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 116 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 2.4496 time to fit residues: 284.2473 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.8974 time to fit residues: 3.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 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: 0.8980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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** 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: 0.7533 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6943 Z= 0.223 Angle : 0.555 10.708 9435 Z= 0.288 Chirality : 0.047 0.446 1071 Planarity : 0.004 0.056 1185 Dihedral : 7.602 171.058 956 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.36 % Allowed : 14.03 % Favored : 84.60 % 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: 0.32 (0.30), residues: 859 helix: 2.27 (0.33), residues: 256 sheet: 0.36 (0.34), residues: 260 loop : -1.56 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 PHE 0.017 0.001 PHE L 211 TYR 0.011 0.001 TYR L 92 ARG 0.003 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: 10 poor density : 107 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 2.3705 time to fit residues: 278.1236 Evaluate side-chains 106 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.3186 time to fit residues: 2.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** 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: 0.7526 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6943 Z= 0.194 Angle : 0.544 10.625 9435 Z= 0.282 Chirality : 0.047 0.441 1071 Planarity : 0.004 0.055 1185 Dihedral : 7.585 171.257 956 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.77 % Allowed : 14.17 % Favored : 84.06 % 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: 0.37 (0.30), residues: 859 helix: 2.32 (0.33), residues: 256 sheet: 0.38 (0.34), residues: 260 loop : -1.52 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.020 0.001 PHE L 211 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 114 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 2.4920 time to fit residues: 278.8936 Evaluate side-chains 107 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.9274 time to fit residues: 5.5128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 H 87 ASN L 102 GLN L 157 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6943 Z= 0.175 Angle : 0.534 10.582 9435 Z= 0.275 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.054 1185 Dihedral : 7.534 171.238 956 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.50 % Allowed : 14.31 % Favored : 84.20 % 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: 0.47 (0.30), residues: 859 helix: 2.33 (0.33), residues: 261 sheet: 0.43 (0.34), residues: 260 loop : -1.45 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 176 HIS 0.002 0.001 HIS L 200 PHE 0.022 0.001 PHE L 211 TYR 0.010 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 115 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 2.4211 time to fit residues: 281.2406 Evaluate side-chains 99 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.3346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** 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: 0.7567 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6943 Z= 0.288 Angle : 0.599 10.920 9435 Z= 0.311 Chirality : 0.048 0.442 1071 Planarity : 0.005 0.054 1185 Dihedral : 7.692 171.510 956 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 0.68 % Allowed : 16.08 % 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: 0.14 (0.29), residues: 859 helix: 2.10 (0.32), residues: 258 sheet: 0.26 (0.34), residues: 260 loop : -1.68 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 176 HIS 0.006 0.001 HIS L 200 PHE 0.023 0.002 PHE L 211 TYR 0.012 0.002 TYR H 98 ARG 0.003 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 100 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 2.4808 time to fit residues: 259.2763 Evaluate side-chains 98 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.3746 time to fit residues: 1.9027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.3980 chunk 10 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.0000 chunk 28 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.1900 ------------------------------------------------------------------------------- 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** L 102 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147753 restraints weight = 21779.432| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.54 r_work: 0.3428 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6943 Z= 0.148 Angle : 0.526 10.478 9435 Z= 0.269 Chirality : 0.046 0.444 1071 Planarity : 0.004 0.053 1185 Dihedral : 7.533 171.996 956 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.95 % Allowed : 15.80 % 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: 0.53 (0.30), residues: 859 helix: 2.40 (0.33), residues: 261 sheet: 0.43 (0.34), residues: 262 loop : -1.42 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 176 HIS 0.002 0.001 HIS H 38 PHE 0.023 0.001 PHE L 211 TYR 0.008 0.001 TYR R 225 ARG 0.002 0.000 ARG N 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6097.19 seconds wall clock time: 107 minutes 7.17 seconds (6427.17 seconds total)