Starting phenix.real_space_refine on Sat Aug 3 13:53:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/08_2024/8hij_34818_neut.cif" } resolution = 3.54 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5304 2.51 5 N 1379 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'THH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.65 Number of scatterers: 8245 At special positions: 0 Unit cell: (66.34, 101.65, 151.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1536 8.00 N 1379 7.00 C 5304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.02 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB THH A 601 " Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 40.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 removed outlier: 3.713A pdb=" N LYS A -64 " --> pdb=" O LYS A -68 " (cutoff:3.500A) Processing helix chain 'A' and resid -57 through -43 Processing helix chain 'A' and resid -38 through -33 removed outlier: 3.828A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.799A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.747A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.759A pdb=" N VAL A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.617A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.856A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.540A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.512A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.936A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.672A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 427 through 451 removed outlier: 3.988A pdb=" N MET A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.570A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.763A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.023A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.930A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.689A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.919A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.919A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.680A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL H 195 " --> pdb=" O HIS H 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.680A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.671A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.923A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 12 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.923A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 12 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA N 97 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.567A pdb=" N LEU L 12 " --> pdb=" O LYS L 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.785A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR L 75 " --> pdb=" O SER L 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.567A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.894A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL L 134 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 147 through 151 removed outlier: 3.634A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR L 194 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS L 196 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1289 1.31 - 1.44: 2457 1.44 - 1.56: 4662 1.56 - 1.69: 2 1.69 - 1.81: 38 Bond restraints: 8448 Sorted by residual: bond pdb=" N THH A 601 " pdb=" C THH A 601 " ideal model delta sigma weight residual 1.346 1.523 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" C4 THH A 601 " pdb=" O4 THH A 601 " ideal model delta sigma weight residual 1.347 1.191 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" C8A THH A 601 " pdb=" N8 THH A 601 " ideal model delta sigma weight residual 1.351 1.499 -0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C6 THH A 601 " pdb=" C9 THH A 601 " ideal model delta sigma weight residual 1.542 1.645 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4A THH A 601 " pdb=" N5 THH A 601 " ideal model delta sigma weight residual 1.419 1.517 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.43: 221 106.43 - 113.37: 4545 113.37 - 120.32: 3120 120.32 - 127.26: 3513 127.26 - 134.21: 94 Bond angle restraints: 11493 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 117.88 -8.07 2.21e+00 2.05e-01 1.33e+01 angle pdb=" C ASN L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta sigma weight residual 121.70 128.02 -6.32 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C PHE N 103 " pdb=" N TYR N 104 " pdb=" CA TYR N 104 " ideal model delta sigma weight residual 122.36 127.05 -4.69 1.42e+00 4.96e-01 1.09e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N PRO A 70 " ideal model delta sigma weight residual 118.44 122.82 -4.38 1.59e+00 3.96e-01 7.59e+00 ... (remaining 11488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4800 15.81 - 31.62: 132 31.62 - 47.43: 39 47.43 - 63.24: 5 63.24 - 79.05: 12 Dihedral angle restraints: 4988 sinusoidal: 1911 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 172.05 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ALA A 17 " pdb=" C ALA A 17 " pdb=" N TYR A 18 " pdb=" CA TYR A 18 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 995 0.050 - 0.101: 236 0.101 - 0.151: 61 0.151 - 0.201: 4 0.201 - 0.252: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP A 107 " pdb=" N TRP A 107 " pdb=" C TRP A 107 " pdb=" CB TRP A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1295 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.014 2.00e-02 2.50e+03 1.39e-02 4.81e+00 pdb=" CG TRP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 103 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A 103 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 103 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 103 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 103 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.033 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO H 109 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.027 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2578 2.83 - 3.35: 7065 3.35 - 3.87: 13375 3.87 - 4.38: 14375 4.38 - 4.90: 25690 Nonbonded interactions: 63083 Sorted by model distance: nonbonded pdb=" OG1 THR A 49 " pdb=" O4 THH A 601 " model vdw 2.315 3.040 nonbonded pdb=" O ARG A 61 " pdb=" OG1 THR A 65 " model vdw 2.330 3.040 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.337 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.341 3.040 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.350 3.040 ... (remaining 63078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.005 0.177 8448 Z= 0.362 Angle : 0.758 8.532 11493 Z= 0.389 Chirality : 0.047 0.252 1298 Planarity : 0.006 0.048 1440 Dihedral : 9.657 76.505 3001 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -3.81 (0.21), residues: 1045 helix: -1.71 (0.19), residues: 384 sheet: -3.00 (0.29), residues: 231 loop : -2.88 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 102 HIS 0.004 0.001 HIS H 38 PHE 0.033 0.002 PHE A 103 TYR 0.026 0.002 TYR A 435 ARG 0.004 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -55 ASP cc_start: 0.6609 (t0) cc_final: 0.6405 (t0) REVERT: A -51 LYS cc_start: 0.8509 (mttt) cc_final: 0.8247 (mttt) REVERT: A -50 MET cc_start: 0.6978 (mmm) cc_final: 0.6731 (mmm) REVERT: A -16 ILE cc_start: 0.8500 (tp) cc_final: 0.8173 (mt) REVERT: A 1 VAL cc_start: 0.8584 (m) cc_final: 0.8263 (p) REVERT: A 46 SER cc_start: 0.7456 (m) cc_final: 0.6633 (t) REVERT: A 81 VAL cc_start: 0.7706 (t) cc_final: 0.7475 (m) REVERT: A 127 SER cc_start: 0.8834 (p) cc_final: 0.8229 (t) REVERT: A 139 TYR cc_start: 0.7092 (t80) cc_final: 0.6886 (t80) REVERT: A 149 TYR cc_start: 0.6915 (t80) cc_final: 0.6580 (t80) REVERT: A 155 TYR cc_start: 0.6982 (m-80) cc_final: 0.6754 (m-80) REVERT: A 162 LEU cc_start: 0.7897 (tp) cc_final: 0.7613 (tp) REVERT: A 254 MET cc_start: 0.7477 (mtt) cc_final: 0.7163 (mtt) REVERT: A 314 THR cc_start: 0.8067 (m) cc_final: 0.7829 (p) REVERT: A 405 PHE cc_start: 0.8105 (t80) cc_final: 0.7820 (t80) REVERT: A 406 PHE cc_start: 0.7492 (m-80) cc_final: 0.6995 (m-80) REVERT: A 411 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7746 (ttpt) REVERT: H 37 LEU cc_start: 0.7269 (mt) cc_final: 0.6950 (mm) REVERT: H 46 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7788 (mmtt) REVERT: H 152 LEU cc_start: 0.7479 (tp) cc_final: 0.7115 (tp) REVERT: N 34 MET cc_start: 0.6920 (mtp) cc_final: 0.6480 (mtp) REVERT: L 4 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6633 (mm-40) REVERT: L 38 GLN cc_start: 0.8298 (tt0) cc_final: 0.8093 (tt0) REVERT: L 73 THR cc_start: 0.8035 (m) cc_final: 0.7832 (t) REVERT: L 83 ASP cc_start: 0.6949 (m-30) cc_final: 0.6615 (m-30) REVERT: L 93 LEU cc_start: 0.7949 (tp) cc_final: 0.7464 (tp) REVERT: L 97 LEU cc_start: 0.8607 (mp) cc_final: 0.8387 (mt) REVERT: L 104 THR cc_start: 0.8497 (p) cc_final: 0.8194 (t) REVERT: L 142 TYR cc_start: 0.7731 (t80) cc_final: 0.7496 (t80) REVERT: L 147 LYS cc_start: 0.7312 (ttmm) cc_final: 0.7103 (ttmm) REVERT: L 211 PHE cc_start: 0.8091 (p90) cc_final: 0.7847 (p90) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2024 time to fit residues: 76.2220 Evaluate side-chains 223 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.0470 chunk 60 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -61 ASN A -3 ASN A 63 GLN A 66 ASN A 99 GLN A 172 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN L 191 HIS L 200 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8448 Z= 0.195 Angle : 0.620 10.820 11493 Z= 0.312 Chirality : 0.043 0.292 1298 Planarity : 0.004 0.046 1440 Dihedral : 5.503 51.777 1184 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.24 % Allowed : 8.96 % Favored : 88.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -2.10 (0.24), residues: 1045 helix: 0.45 (0.25), residues: 381 sheet: -2.47 (0.30), residues: 245 loop : -2.38 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 102 HIS 0.003 0.001 HIS A 355 PHE 0.017 0.002 PHE A 103 TYR 0.023 0.001 TYR A 438 ARG 0.006 0.000 ARG A -21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A -51 LYS cc_start: 0.8712 (mttt) cc_final: 0.8392 (mttt) REVERT: A -16 ILE cc_start: 0.8443 (tp) cc_final: 0.8240 (mt) REVERT: A -12 GLN cc_start: 0.7733 (mt0) cc_final: 0.7440 (tt0) REVERT: A 1 VAL cc_start: 0.8588 (m) cc_final: 0.8380 (p) REVERT: A 11 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7023 (tm) REVERT: A 46 SER cc_start: 0.7526 (m) cc_final: 0.7075 (t) REVERT: A 76 TYR cc_start: 0.8675 (t80) cc_final: 0.8358 (t80) REVERT: A 127 SER cc_start: 0.8740 (p) cc_final: 0.8200 (t) REVERT: A 128 VAL cc_start: 0.8333 (t) cc_final: 0.8006 (p) REVERT: A 162 LEU cc_start: 0.8069 (tp) cc_final: 0.7806 (tp) REVERT: A 204 LYS cc_start: 0.7684 (tttt) cc_final: 0.7388 (tttt) REVERT: A 254 MET cc_start: 0.7564 (mtt) cc_final: 0.7148 (mtt) REVERT: A 314 THR cc_start: 0.8157 (m) cc_final: 0.7875 (p) REVERT: A 394 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 398 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8613 (mm) REVERT: A 405 PHE cc_start: 0.8189 (t80) cc_final: 0.7857 (t80) REVERT: A 406 PHE cc_start: 0.7591 (m-80) cc_final: 0.7113 (m-10) REVERT: H 70 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7966 (ttp80) REVERT: H 80 ASN cc_start: 0.8262 (t0) cc_final: 0.7987 (t0) REVERT: H 98 TYR cc_start: 0.8579 (m-80) cc_final: 0.8265 (m-80) REVERT: H 152 LEU cc_start: 0.7661 (tp) cc_final: 0.7446 (tp) REVERT: H 159 TYR cc_start: 0.7700 (p90) cc_final: 0.7092 (p90) REVERT: N 34 MET cc_start: 0.6869 (mtp) cc_final: 0.6421 (mtp) REVERT: N 89 GLU cc_start: 0.7363 (mp0) cc_final: 0.7072 (mp0) REVERT: L 4 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6689 (mm-40) REVERT: L 73 THR cc_start: 0.8063 (m) cc_final: 0.7520 (p) REVERT: L 83 ASP cc_start: 0.7309 (m-30) cc_final: 0.6997 (m-30) REVERT: L 97 LEU cc_start: 0.8562 (mp) cc_final: 0.8354 (mt) REVERT: L 120 PHE cc_start: 0.7797 (m-80) cc_final: 0.7583 (m-80) REVERT: L 142 TYR cc_start: 0.8035 (t80) cc_final: 0.7760 (t80) REVERT: L 145 GLU cc_start: 0.7507 (mp0) cc_final: 0.7120 (mp0) REVERT: L 172 ASP cc_start: 0.8499 (p0) cc_final: 0.8206 (p0) REVERT: L 190 LYS cc_start: 0.7476 (ttpp) cc_final: 0.6969 (ttpp) REVERT: L 192 LYS cc_start: 0.4891 (tppt) cc_final: 0.4529 (tppt) REVERT: L 211 PHE cc_start: 0.8233 (p90) cc_final: 0.7935 (p90) outliers start: 20 outliers final: 9 residues processed: 243 average time/residue: 0.2132 time to fit residues: 69.2057 Evaluate side-chains 239 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN A 186 ASN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8448 Z= 0.277 Angle : 0.615 7.825 11493 Z= 0.315 Chirality : 0.043 0.250 1298 Planarity : 0.004 0.037 1440 Dihedral : 5.479 48.766 1184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.69 % Allowed : 11.31 % Favored : 86.00 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -1.41 (0.25), residues: 1045 helix: 0.97 (0.25), residues: 382 sheet: -2.14 (0.31), residues: 233 loop : -1.94 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 102 HIS 0.005 0.001 HIS A 355 PHE 0.014 0.002 PHE A -18 TYR 0.027 0.002 TYR A 286 ARG 0.003 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -57 VAL cc_start: 0.7013 (m) cc_final: 0.6792 (p) REVERT: A -51 LYS cc_start: 0.8605 (mttt) cc_final: 0.8355 (mttt) REVERT: A -6 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7969 (ttpt) REVERT: A 1 VAL cc_start: 0.8675 (m) cc_final: 0.8471 (p) REVERT: A 11 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7094 (tm) REVERT: A 46 SER cc_start: 0.7501 (m) cc_final: 0.7214 (t) REVERT: A 112 LEU cc_start: 0.7098 (mt) cc_final: 0.6888 (mt) REVERT: A 122 MET cc_start: 0.7136 (tmm) cc_final: 0.6884 (ppp) REVERT: A 127 SER cc_start: 0.8728 (p) cc_final: 0.8317 (t) REVERT: A 162 LEU cc_start: 0.8132 (tp) cc_final: 0.7869 (tp) REVERT: A 254 MET cc_start: 0.7665 (mtt) cc_final: 0.7204 (mtt) REVERT: A 314 THR cc_start: 0.8136 (m) cc_final: 0.7875 (p) REVERT: A 326 PHE cc_start: 0.6698 (m-10) cc_final: 0.6419 (m-10) REVERT: A 394 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 405 PHE cc_start: 0.8250 (t80) cc_final: 0.7942 (t80) REVERT: A 406 PHE cc_start: 0.7596 (m-80) cc_final: 0.7144 (m-10) REVERT: A 445 ILE cc_start: 0.6861 (mt) cc_final: 0.6611 (mt) REVERT: H 15 VAL cc_start: 0.8245 (m) cc_final: 0.7997 (p) REVERT: H 70 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8221 (ttp80) REVERT: H 74 SER cc_start: 0.7863 (t) cc_final: 0.7256 (p) REVERT: H 80 ASN cc_start: 0.8305 (t0) cc_final: 0.7968 (t0) REVERT: H 98 TYR cc_start: 0.8619 (m-80) cc_final: 0.8276 (m-80) REVERT: H 131 LYS cc_start: 0.7657 (ptmm) cc_final: 0.7354 (ptpp) REVERT: H 138 LEU cc_start: 0.8317 (mt) cc_final: 0.8106 (mt) REVERT: N 34 MET cc_start: 0.6923 (mtp) cc_final: 0.6464 (mtp) REVERT: N 89 GLU cc_start: 0.7512 (mp0) cc_final: 0.7121 (mp0) REVERT: L 4 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6826 (mm-40) REVERT: L 53 SER cc_start: 0.8158 (m) cc_final: 0.7920 (t) REVERT: L 68 SER cc_start: 0.7884 (m) cc_final: 0.7449 (p) REVERT: L 87 TYR cc_start: 0.8378 (m-80) cc_final: 0.8120 (m-80) REVERT: L 91 GLN cc_start: 0.8499 (pp30) cc_final: 0.8242 (pp30) REVERT: L 97 LEU cc_start: 0.8621 (mp) cc_final: 0.8359 (mt) REVERT: L 172 ASP cc_start: 0.8443 (p0) cc_final: 0.8231 (p0) REVERT: L 175 TYR cc_start: 0.7962 (m-10) cc_final: 0.7326 (m-10) REVERT: L 190 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6940 (ttpp) REVERT: L 211 PHE cc_start: 0.8275 (p90) cc_final: 0.7925 (p90) outliers start: 24 outliers final: 17 residues processed: 255 average time/residue: 0.2127 time to fit residues: 72.4722 Evaluate side-chains 256 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 0.0060 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A 66 ASN H 178 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8448 Z= 0.201 Angle : 0.594 7.993 11493 Z= 0.297 Chirality : 0.043 0.236 1298 Planarity : 0.004 0.039 1440 Dihedral : 5.152 45.918 1184 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.92 % Allowed : 12.88 % Favored : 83.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -0.96 (0.26), residues: 1045 helix: 1.34 (0.25), residues: 381 sheet: -1.88 (0.32), residues: 234 loop : -1.68 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 270 HIS 0.005 0.001 HIS A 355 PHE 0.011 0.001 PHE A 372 TYR 0.027 0.001 TYR A 286 ARG 0.006 0.000 ARG A -21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -57 VAL cc_start: 0.6938 (m) cc_final: 0.6643 (p) REVERT: A -51 LYS cc_start: 0.8641 (mttt) cc_final: 0.8381 (mttt) REVERT: A -12 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: A -6 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7924 (ttpt) REVERT: A 1 VAL cc_start: 0.8675 (m) cc_final: 0.8438 (p) REVERT: A 11 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7118 (tm) REVERT: A 46 SER cc_start: 0.7464 (m) cc_final: 0.7153 (t) REVERT: A 72 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.5710 (tt) REVERT: A 127 SER cc_start: 0.8749 (p) cc_final: 0.8341 (t) REVERT: A 162 LEU cc_start: 0.8151 (tp) cc_final: 0.7921 (tp) REVERT: A 211 PHE cc_start: 0.7938 (m-80) cc_final: 0.7356 (m-80) REVERT: A 254 MET cc_start: 0.7652 (mtt) cc_final: 0.7194 (mtt) REVERT: A 293 ASN cc_start: 0.7942 (t0) cc_final: 0.7558 (t0) REVERT: A 314 THR cc_start: 0.8113 (m) cc_final: 0.7864 (p) REVERT: A 326 PHE cc_start: 0.6670 (m-10) cc_final: 0.6401 (m-10) REVERT: A 346 GLN cc_start: 0.7645 (mt0) cc_final: 0.7419 (mt0) REVERT: A 394 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 405 PHE cc_start: 0.8266 (t80) cc_final: 0.7971 (t80) REVERT: A 406 PHE cc_start: 0.7582 (m-80) cc_final: 0.7157 (m-10) REVERT: A 445 ILE cc_start: 0.6882 (mt) cc_final: 0.6633 (mt) REVERT: H 70 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8271 (ttp80) REVERT: H 74 SER cc_start: 0.7898 (t) cc_final: 0.7334 (p) REVERT: H 80 ASN cc_start: 0.8273 (t0) cc_final: 0.7975 (t0) REVERT: H 98 TYR cc_start: 0.8577 (m-80) cc_final: 0.8203 (m-80) REVERT: H 131 LYS cc_start: 0.7488 (ptmm) cc_final: 0.7184 (ptpp) REVERT: N 34 MET cc_start: 0.6949 (mtp) cc_final: 0.6457 (mtp) REVERT: N 89 GLU cc_start: 0.7528 (mp0) cc_final: 0.7095 (mp0) REVERT: N 90 ASP cc_start: 0.7665 (t0) cc_final: 0.7460 (t0) REVERT: L 4 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6718 (mm-40) REVERT: L 53 SER cc_start: 0.8146 (m) cc_final: 0.7932 (t) REVERT: L 68 SER cc_start: 0.7953 (m) cc_final: 0.7497 (p) REVERT: L 87 TYR cc_start: 0.8316 (m-80) cc_final: 0.7998 (m-80) REVERT: L 91 GLN cc_start: 0.8600 (pp30) cc_final: 0.8316 (pp30) REVERT: L 97 LEU cc_start: 0.8565 (mp) cc_final: 0.8329 (mt) REVERT: L 175 TYR cc_start: 0.7876 (m-10) cc_final: 0.7517 (m-10) REVERT: L 190 LYS cc_start: 0.7464 (ttpp) cc_final: 0.6863 (ttpp) REVERT: L 211 PHE cc_start: 0.8322 (p90) cc_final: 0.7868 (p90) outliers start: 35 outliers final: 21 residues processed: 252 average time/residue: 0.2065 time to fit residues: 69.6645 Evaluate side-chains 255 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -12 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8448 Z= 0.212 Angle : 0.602 7.588 11493 Z= 0.301 Chirality : 0.042 0.201 1298 Planarity : 0.004 0.038 1440 Dihedral : 5.076 45.720 1184 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.14 % Allowed : 13.89 % Favored : 81.97 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -0.73 (0.26), residues: 1045 helix: 1.49 (0.25), residues: 381 sheet: -1.74 (0.32), residues: 234 loop : -1.52 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 292 HIS 0.005 0.001 HIS A 355 PHE 0.022 0.001 PHE A 37 TYR 0.033 0.002 TYR A 286 ARG 0.002 0.000 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A -57 VAL cc_start: 0.6966 (m) cc_final: 0.6640 (p) REVERT: A -51 LYS cc_start: 0.8504 (mttt) cc_final: 0.8298 (mttt) REVERT: A -36 LYS cc_start: 0.8068 (mppt) cc_final: 0.7604 (ttmm) REVERT: A -6 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7933 (ttpt) REVERT: A 0 LYS cc_start: 0.7924 (mttm) cc_final: 0.7089 (mttm) REVERT: A 1 VAL cc_start: 0.8661 (m) cc_final: 0.8391 (p) REVERT: A 3 GLU cc_start: 0.7489 (mp0) cc_final: 0.6868 (mp0) REVERT: A 21 LYS cc_start: 0.8330 (tttm) cc_final: 0.8128 (tttm) REVERT: A 46 SER cc_start: 0.7448 (m) cc_final: 0.7196 (t) REVERT: A 72 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6809 (tt) REVERT: A 123 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: A 127 SER cc_start: 0.8704 (p) cc_final: 0.8399 (t) REVERT: A 162 LEU cc_start: 0.8154 (tp) cc_final: 0.7925 (tp) REVERT: A 211 PHE cc_start: 0.7891 (m-80) cc_final: 0.7321 (m-80) REVERT: A 254 MET cc_start: 0.7700 (mtt) cc_final: 0.7203 (mtt) REVERT: A 293 ASN cc_start: 0.7999 (t0) cc_final: 0.7656 (t0) REVERT: A 326 PHE cc_start: 0.6682 (m-10) cc_final: 0.6463 (m-10) REVERT: A 346 GLN cc_start: 0.7738 (mt0) cc_final: 0.7464 (mt0) REVERT: A 394 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 405 PHE cc_start: 0.8284 (t80) cc_final: 0.7819 (t80) REVERT: A 408 THR cc_start: 0.8554 (m) cc_final: 0.8234 (p) REVERT: A 445 ILE cc_start: 0.6928 (mt) cc_final: 0.6673 (mt) REVERT: H 35 PHE cc_start: 0.6913 (m-80) cc_final: 0.6417 (m-80) REVERT: H 70 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8263 (ttp80) REVERT: H 74 SER cc_start: 0.7931 (t) cc_final: 0.7390 (p) REVERT: H 98 TYR cc_start: 0.8620 (m-80) cc_final: 0.8230 (m-80) REVERT: H 131 LYS cc_start: 0.7502 (ptmm) cc_final: 0.7198 (ptpp) REVERT: N 34 MET cc_start: 0.6963 (mtp) cc_final: 0.6470 (mtp) REVERT: N 60 TYR cc_start: 0.8367 (m-10) cc_final: 0.7844 (m-80) REVERT: N 89 GLU cc_start: 0.7599 (mp0) cc_final: 0.7130 (mp0) REVERT: L 4 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6697 (mm-40) REVERT: L 68 SER cc_start: 0.8073 (m) cc_final: 0.7582 (p) REVERT: L 87 TYR cc_start: 0.8377 (m-80) cc_final: 0.8024 (m-80) REVERT: L 90 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7181 (tt0) REVERT: L 97 LEU cc_start: 0.8503 (mp) cc_final: 0.8234 (mt) REVERT: L 145 GLU cc_start: 0.7580 (mp0) cc_final: 0.6981 (mp0) REVERT: L 148 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8338 (m) REVERT: L 175 TYR cc_start: 0.7922 (m-10) cc_final: 0.7554 (m-10) REVERT: L 190 LYS cc_start: 0.7444 (ttpp) cc_final: 0.6811 (ttpp) REVERT: L 192 LYS cc_start: 0.5171 (OUTLIER) cc_final: 0.4937 (tptt) REVERT: L 211 PHE cc_start: 0.8339 (p90) cc_final: 0.7858 (p90) outliers start: 37 outliers final: 25 residues processed: 248 average time/residue: 0.2221 time to fit residues: 72.7166 Evaluate side-chains 251 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 192 LYS Chi-restraints excluded: chain L residue 199 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN ** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8448 Z= 0.263 Angle : 0.643 8.101 11493 Z= 0.324 Chirality : 0.043 0.214 1298 Planarity : 0.004 0.038 1440 Dihedral : 5.122 46.222 1184 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.14 % Allowed : 14.45 % Favored : 81.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -0.60 (0.26), residues: 1045 helix: 1.46 (0.25), residues: 385 sheet: -1.56 (0.32), residues: 241 loop : -1.39 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 292 HIS 0.005 0.001 HIS A 355 PHE 0.029 0.002 PHE A 37 TYR 0.034 0.002 TYR A 286 ARG 0.003 0.000 ARG N 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -57 VAL cc_start: 0.6989 (m) cc_final: 0.6681 (p) REVERT: A -32 LYS cc_start: 0.6638 (pttt) cc_final: 0.6403 (pttt) REVERT: A 1 VAL cc_start: 0.8690 (m) cc_final: 0.8374 (p) REVERT: A 2 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7746 (ptpt) REVERT: A 3 GLU cc_start: 0.7539 (mp0) cc_final: 0.6848 (mp0) REVERT: A 11 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7267 (tm) REVERT: A 15 ARG cc_start: 0.6634 (tmm160) cc_final: 0.6374 (tmm160) REVERT: A 21 LYS cc_start: 0.8384 (tttm) cc_final: 0.8176 (tttm) REVERT: A 46 SER cc_start: 0.7550 (m) cc_final: 0.7255 (t) REVERT: A 127 SER cc_start: 0.8750 (p) cc_final: 0.8322 (t) REVERT: A 162 LEU cc_start: 0.8189 (tp) cc_final: 0.7975 (tp) REVERT: A 172 GLN cc_start: 0.7923 (tp40) cc_final: 0.7699 (tm-30) REVERT: A 176 THR cc_start: 0.8105 (t) cc_final: 0.7555 (p) REVERT: A 211 PHE cc_start: 0.7913 (m-80) cc_final: 0.7131 (m-80) REVERT: A 254 MET cc_start: 0.7712 (mtt) cc_final: 0.7200 (mtt) REVERT: A 293 ASN cc_start: 0.8064 (t0) cc_final: 0.7747 (t0) REVERT: A 326 PHE cc_start: 0.6732 (m-10) cc_final: 0.6509 (m-10) REVERT: A 346 GLN cc_start: 0.7799 (mt0) cc_final: 0.7468 (mt0) REVERT: A 370 VAL cc_start: 0.8713 (t) cc_final: 0.8508 (p) REVERT: A 394 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 405 PHE cc_start: 0.8251 (t80) cc_final: 0.7879 (t80) REVERT: A 408 THR cc_start: 0.8620 (m) cc_final: 0.8387 (t) REVERT: A 445 ILE cc_start: 0.7044 (mt) cc_final: 0.6785 (mt) REVERT: H 35 PHE cc_start: 0.7020 (m-80) cc_final: 0.6546 (m-80) REVERT: H 74 SER cc_start: 0.7989 (t) cc_final: 0.7465 (p) REVERT: H 131 LYS cc_start: 0.7558 (ptmm) cc_final: 0.7238 (ptpp) REVERT: N 34 MET cc_start: 0.6971 (mtp) cc_final: 0.6477 (mtp) REVERT: N 89 GLU cc_start: 0.7642 (mp0) cc_final: 0.7182 (mp0) REVERT: L 4 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6780 (mm-40) REVERT: L 43 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8387 (mtmm) REVERT: L 87 TYR cc_start: 0.8416 (m-80) cc_final: 0.7973 (m-80) REVERT: L 90 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7095 (tt0) REVERT: L 97 LEU cc_start: 0.8487 (mp) cc_final: 0.8228 (mt) REVERT: L 145 GLU cc_start: 0.7656 (mp0) cc_final: 0.7064 (mp0) REVERT: L 175 TYR cc_start: 0.8013 (m-10) cc_final: 0.7680 (m-10) REVERT: L 190 LYS cc_start: 0.7504 (ttpp) cc_final: 0.6884 (ttpp) outliers start: 37 outliers final: 25 residues processed: 239 average time/residue: 0.2131 time to fit residues: 67.9206 Evaluate side-chains 241 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4594 > 50: distance: 18 - 40: 5.114 distance: 22 - 48: 5.373 distance: 27 - 53: 7.381 distance: 34 - 40: 6.948 distance: 40 - 41: 4.348 distance: 41 - 42: 7.283 distance: 41 - 44: 18.313 distance: 42 - 43: 5.043 distance: 42 - 48: 3.738 distance: 44 - 45: 17.425 distance: 45 - 46: 7.001 distance: 45 - 47: 3.997 distance: 48 - 49: 14.227 distance: 49 - 50: 9.766 distance: 49 - 52: 10.827 distance: 50 - 51: 3.802 distance: 50 - 53: 4.372 distance: 53 - 54: 8.039 distance: 54 - 55: 6.642 distance: 54 - 57: 6.695 distance: 55 - 56: 4.560 distance: 55 - 63: 10.012 distance: 57 - 58: 9.916 distance: 58 - 59: 7.059 distance: 59 - 61: 6.005 distance: 61 - 62: 3.129 distance: 63 - 64: 5.678 distance: 64 - 65: 4.645 distance: 65 - 66: 5.844 distance: 65 - 70: 8.337 distance: 67 - 68: 6.554 distance: 67 - 69: 10.777 distance: 70 - 71: 3.076 distance: 71 - 72: 21.913 distance: 71 - 74: 15.152 distance: 72 - 73: 22.982 distance: 72 - 81: 15.857 distance: 74 - 75: 13.522 distance: 75 - 76: 3.197 distance: 76 - 77: 6.991 distance: 77 - 78: 10.566 distance: 78 - 79: 10.831 distance: 78 - 80: 11.332 distance: 81 - 82: 5.322 distance: 82 - 83: 14.383 distance: 82 - 85: 12.661 distance: 83 - 84: 15.051 distance: 83 - 91: 15.764 distance: 85 - 86: 17.363 distance: 86 - 87: 10.041 distance: 86 - 88: 7.155 distance: 87 - 89: 5.207 distance: 88 - 90: 7.059 distance: 89 - 90: 6.103 distance: 91 - 92: 15.295 distance: 91 - 97: 9.838 distance: 92 - 93: 13.914 distance: 92 - 95: 23.081 distance: 93 - 94: 23.514 distance: 93 - 98: 9.444 distance: 95 - 96: 5.912 distance: 96 - 97: 32.180 distance: 98 - 99: 4.219 distance: 99 - 100: 3.911 distance: 99 - 102: 8.774 distance: 100 - 101: 15.888 distance: 100 - 104: 7.597 distance: 102 - 103: 20.778 distance: 104 - 105: 11.848 distance: 105 - 106: 4.071 distance: 105 - 108: 12.590 distance: 106 - 107: 14.948 distance: 106 - 110: 4.308 distance: 107 - 133: 23.828 distance: 108 - 109: 30.281 distance: 110 - 111: 7.987 distance: 111 - 112: 5.404 distance: 111 - 114: 11.825 distance: 112 - 113: 8.505 distance: 112 - 118: 5.360 distance: 113 - 139: 7.442 distance: 114 - 115: 17.680 distance: 114 - 116: 9.024 distance: 115 - 117: 9.701