Starting phenix.real_space_refine on Mon Mar 11 02:42:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m71_23707/03_2024/7m71_23707.pdb" } resolution = 2.66 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= -0.003 sd= 0.072 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 29 5.16 5 C 4212 2.51 5 N 1112 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 214": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L ARG 211": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6646 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "B" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.28, per 1000 atoms: 0.64 Number of scatterers: 6646 At special positions: 0 Unit cell: (115.193, 92.6293, 129.444, 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 29 16.00 O 1293 8.00 N 1112 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 222 " - pdb=" SG CYS L 214 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 20 sheets defined 14.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.606A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.446A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.860A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.715A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.504A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.268A pdb=" N GLY H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.906A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.703A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.761A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.776A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.893A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 137 through 138 removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.410A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 148 Processing sheet with id=AC2, first strand: chain 'L' and resid 161 through 164 removed outlier: 4.153A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 465 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: 1.92 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1616 1.33 - 1.45: 1469 1.45 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6810 Sorted by residual: bond pdb=" CA PHE L 118 " pdb=" C PHE L 118 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.06e-02 8.90e+03 1.55e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CZ ARG A 454 " pdb=" NH2 ARG A 454 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA PRO L 119 " pdb=" C PRO L 119 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.33: 367 107.33 - 114.23: 3395 114.23 - 121.14: 3478 121.14 - 128.05: 1976 128.05 - 134.96: 42 Bond angle restraints: 9258 Sorted by residual: angle pdb=" CA PHE H 68 " pdb=" CB PHE H 68 " pdb=" CG PHE H 68 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 114.23 120.16 -5.93 8.80e-01 1.29e+00 4.54e+01 angle pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " pdb=" ND2 ASN A 331 " ideal model delta sigma weight residual 116.40 107.47 8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C LYS H 215 " pdb=" N LYS H 216 " pdb=" CA LYS H 216 " ideal model delta sigma weight residual 120.95 128.90 -7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" CA PHE L 209 " pdb=" CB PHE L 209 " pdb=" CG PHE L 209 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3785 17.69 - 35.37: 271 35.37 - 53.05: 45 53.05 - 70.74: 10 70.74 - 88.42: 4 Dihedral angle restraints: 4115 sinusoidal: 1642 harmonic: 2473 Sorted by residual: dihedral pdb=" CA THR L 178 " pdb=" C THR L 178 " pdb=" N LEU L 179 " pdb=" CA LEU L 179 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU L 104 " pdb=" C LEU L 104 " pdb=" N GLU L 105 " pdb=" CA GLU L 105 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 4112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 1010 0.274 - 0.548: 13 0.548 - 0.822: 0 0.822 - 1.096: 0 1.096 - 1.370: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.69e+01 chirality pdb=" CA ASP H 150 " pdb=" N ASP H 150 " pdb=" C ASP H 150 " pdb=" CB ASP H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 1021 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.098 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN A 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " 0.131 2.00e-02 2.50e+03 7.39e-02 1.09e+02 pdb=" CG TYR L 49 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.121 2.00e-02 2.50e+03 6.35e-02 1.01e+02 pdb=" CG TRP B 353 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.074 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3298 3.00 - 3.48: 6121 3.48 - 3.95: 11157 3.95 - 4.43: 12531 4.43 - 4.90: 20762 Nonbonded interactions: 53869 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.531 2.440 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.549 2.440 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.561 2.440 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.577 2.440 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.579 2.440 ... (remaining 53864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.410 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: 0.010 Extract box with map and model: 9.990 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.013 0.073 6810 Z= 0.828 Angle : 1.861 9.223 9258 Z= 1.235 Chirality : 0.112 1.370 1024 Planarity : 0.016 0.190 1193 Dihedral : 12.979 88.419 2502 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 3.81 % Favored : 95.78 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 2.17 % 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: -0.93 (0.27), residues: 844 helix: -4.22 (0.28), residues: 79 sheet: 0.09 (0.32), residues: 253 loop : -0.31 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.024 TRP B 353 HIS 0.007 0.003 HIS H 206 PHE 0.077 0.013 PHE L 118 TYR 0.131 0.019 TYR L 49 ARG 0.011 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.715 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 1.6725 time to fit residues: 97.6090 Evaluate side-chains 27 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 487 ASN B 354 ASN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6810 Z= 0.176 Angle : 0.625 8.482 9258 Z= 0.328 Chirality : 0.045 0.147 1024 Planarity : 0.005 0.039 1193 Dihedral : 6.195 48.075 1017 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.95 % Allowed : 7.76 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.29), residues: 844 helix: -3.04 (0.59), residues: 65 sheet: 0.20 (0.30), residues: 279 loop : 0.00 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.001 HIS L 198 PHE 0.015 0.001 PHE B 497 TYR 0.025 0.001 TYR L 186 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.846 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 38 average time/residue: 1.5984 time to fit residues: 63.9457 Evaluate side-chains 26 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN L 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 6810 Z= 0.466 Angle : 0.664 6.796 9258 Z= 0.349 Chirality : 0.047 0.155 1024 Planarity : 0.005 0.043 1193 Dihedral : 6.280 47.426 1014 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.82 % Allowed : 9.52 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.59 (0.29), residues: 844 helix: -2.92 (0.52), residues: 78 sheet: 0.01 (0.30), residues: 284 loop : -0.08 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.015 0.002 PHE L 83 TYR 0.024 0.002 TYR A 495 ARG 0.010 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.841 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 31 average time/residue: 1.6784 time to fit residues: 54.9680 Evaluate side-chains 27 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6810 Z= 0.313 Angle : 0.587 6.842 9258 Z= 0.305 Chirality : 0.044 0.145 1024 Planarity : 0.004 0.047 1193 Dihedral : 5.863 48.682 1014 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.09 % Allowed : 10.61 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.59 (0.29), residues: 844 helix: -2.93 (0.55), residues: 72 sheet: 0.05 (0.31), residues: 276 loop : -0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.001 PHE H 29 TYR 0.017 0.001 TYR L 186 ARG 0.008 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: H 203 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6112 (p0) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 1.4329 time to fit residues: 47.2863 Evaluate side-chains 25 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 0.0170 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6810 Z= 0.350 Angle : 0.592 6.500 9258 Z= 0.308 Chirality : 0.044 0.141 1024 Planarity : 0.004 0.047 1193 Dihedral : 5.858 49.171 1014 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.50 % Allowed : 11.02 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.61 (0.29), residues: 844 helix: -3.15 (0.52), residues: 72 sheet: 0.15 (0.31), residues: 275 loop : -0.21 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.001 0.001 HIS L 189 PHE 0.013 0.001 PHE H 29 TYR 0.017 0.001 TYR L 186 ARG 0.010 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 0.847 Fit side-chains REVERT: H 203 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.6287 (p0) REVERT: L 187 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8591 (mp0) outliers start: 11 outliers final: 6 residues processed: 33 average time/residue: 1.3913 time to fit residues: 48.9816 Evaluate side-chains 27 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6810 Z= 0.181 Angle : 0.542 7.055 9258 Z= 0.279 Chirality : 0.043 0.147 1024 Planarity : 0.004 0.048 1193 Dihedral : 5.361 50.611 1014 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.09 % Allowed : 11.70 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.29), residues: 844 helix: -2.92 (0.57), residues: 66 sheet: 0.31 (0.32), residues: 255 loop : -0.11 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.000 HIS A 519 PHE 0.013 0.001 PHE H 29 TYR 0.015 0.001 TYR L 186 ARG 0.009 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.771 Fit side-chains REVERT: H 201 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8922 (pp) REVERT: H 203 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6481 (p0) REVERT: L 187 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8503 (mp0) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 1.4028 time to fit residues: 47.8125 Evaluate side-chains 26 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6810 Z= 0.244 Angle : 0.561 7.001 9258 Z= 0.288 Chirality : 0.044 0.154 1024 Planarity : 0.004 0.048 1193 Dihedral : 5.354 50.653 1014 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.50 % Allowed : 11.43 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.44 (0.29), residues: 844 helix: -2.91 (0.57), residues: 66 sheet: 0.07 (0.31), residues: 274 loop : -0.02 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS L 189 PHE 0.011 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.012 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 22 time to evaluate : 0.756 Fit side-chains REVERT: H 201 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8920 (pp) REVERT: L 187 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8557 (mp0) outliers start: 11 outliers final: 5 residues processed: 33 average time/residue: 1.4843 time to fit residues: 51.8825 Evaluate side-chains 25 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6810 Z= 0.285 Angle : 0.576 7.585 9258 Z= 0.297 Chirality : 0.044 0.145 1024 Planarity : 0.004 0.053 1193 Dihedral : 5.442 50.386 1014 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.09 % Allowed : 12.79 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.29), residues: 844 helix: -2.91 (0.54), residues: 72 sheet: 0.05 (0.31), residues: 284 loop : -0.08 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.012 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 187 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8570 (mp0) outliers start: 8 outliers final: 6 residues processed: 31 average time/residue: 1.7089 time to fit residues: 55.8831 Evaluate side-chains 28 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6810 Z= 0.243 Angle : 0.566 7.593 9258 Z= 0.291 Chirality : 0.044 0.137 1024 Planarity : 0.004 0.052 1193 Dihedral : 5.356 50.597 1014 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.09 % Allowed : 12.65 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 844 helix: -2.89 (0.57), residues: 66 sheet: 0.09 (0.32), residues: 274 loop : -0.01 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS H 206 PHE 0.011 0.001 PHE H 29 TYR 0.015 0.001 TYR L 186 ARG 0.013 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 187 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8585 (mp0) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 1.7711 time to fit residues: 59.5587 Evaluate side-chains 29 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN L 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6810 Z= 0.256 Angle : 0.571 7.785 9258 Z= 0.294 Chirality : 0.044 0.147 1024 Planarity : 0.004 0.056 1193 Dihedral : 5.372 50.595 1014 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.82 % Allowed : 13.06 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.51 (0.29), residues: 844 helix: -2.85 (0.55), residues: 72 sheet: 0.04 (0.31), residues: 279 loop : -0.05 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE H 29 TYR 0.014 0.001 TYR L 186 ARG 0.013 0.001 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: L 187 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8678 (mp0) outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 1.7489 time to fit residues: 53.5251 Evaluate side-chains 28 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.0000 chunk 75 optimal weight: 20.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.053716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.034764 restraints weight = 33232.022| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.48 r_work: 0.2768 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6810 Z= 0.135 Angle : 0.537 7.229 9258 Z= 0.273 Chirality : 0.043 0.137 1024 Planarity : 0.004 0.047 1193 Dihedral : 4.960 51.832 1014 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.68 % Allowed : 13.33 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.17 (0.29), residues: 844 helix: -2.77 (0.58), residues: 66 sheet: 0.43 (0.34), residues: 252 loop : 0.07 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS H 206 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR A 369 ARG 0.013 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.61 seconds wall clock time: 41 minutes 20.49 seconds (2480.49 seconds total)