Starting phenix.real_space_refine on Sun Feb 18 22:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/02_2024/7nri_12546_trim_updated.pdb" } resolution = 3.03 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= 0.012 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7430 2.51 5 N 2014 2.21 5 O 2316 1.98 5 H 11351 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 421": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 497": "OD1" <-> "OD2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A ARG 526": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A ASP 624": "OD1" <-> "OD2" Residue "A ARG 661": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 795": "OD1" <-> "OD2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 38": "OD1" <-> "OD2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23143 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12128 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 5416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5416 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 844 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3346 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1291 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.23, per 1000 atoms: 0.44 Number of scatterers: 23143 At special positions: 0 Unit cell: (99.22, 133.66, 125.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2316 8.00 N 2014 7.00 C 7430 6.00 H 11351 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 15 sheets defined 18.8% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 130 through 144 Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.438A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 4.237A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.372A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 49 through 60 removed outlier: 4.095A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 161 through 188 removed outlier: 3.825A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 209 through 212 No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 228 through 240 removed outlier: 4.060A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.035A pdb=" N LEU A 84 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 32 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 86 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 8.537A pdb=" N THR A 98 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 165 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER A 100 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 167 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 329 removed outlier: 6.284A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.742A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.327A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 398 through 404 removed outlier: 6.527A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.782A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 433 removed outlier: 5.076A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 784 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.667A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.598A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.898A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 122 through 124 Processing sheet with id= J, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.664A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= L, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.791A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 290 through 292 Processing sheet with id= N, first strand: chain 'B' and resid 331 through 333 Processing sheet with id= O, first strand: chain 'E' and resid 32 through 35 450 hydrogen bonds defined for protein. 1248 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: 8.37 Time building geometry restraints manager: 20.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11319 1.03 - 1.22: 33 1.22 - 1.42: 5212 1.42 - 1.61: 6775 1.61 - 1.80: 63 Bond restraints: 23402 Sorted by residual: bond pdb=" C TRP G 1 " pdb=" N ASN G 2 " ideal model delta sigma weight residual 1.329 1.452 -0.123 1.40e-02 5.10e+03 7.78e+01 bond pdb=" CD2 PHE G 7 " pdb=" HD2 PHE G 7 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CZ PHE G 7 " pdb=" HZ PHE G 7 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CD1 PHE G 7 " pdb=" HD1 PHE G 7 " ideal model delta sigma weight residual 0.930 1.088 -0.158 2.00e-02 2.50e+03 6.27e+01 bond pdb=" CE1 PHE G 7 " pdb=" HE1 PHE G 7 " ideal model delta sigma weight residual 0.930 1.088 -0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 23397 not shown) Histogram of bond angle deviations from ideal: 92.90 - 101.12: 28 101.12 - 109.35: 14683 109.35 - 117.58: 15800 117.58 - 125.81: 11322 125.81 - 134.03: 251 Bond angle restraints: 42084 Sorted by residual: angle pdb=" CA TRP G 1 " pdb=" CB TRP G 1 " pdb=" CG TRP G 1 " ideal model delta sigma weight residual 113.60 97.20 16.40 1.90e+00 2.77e-01 7.45e+01 angle pdb=" CB TRP G 1 " pdb=" CG TRP G 1 " pdb=" CD2 TRP G 1 " ideal model delta sigma weight residual 126.80 116.51 10.29 1.40e+00 5.10e-01 5.41e+01 angle pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " pdb=" O9 UX8 G 3 " ideal model delta sigma weight residual 108.58 92.90 15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" CA SER G 4 " pdb=" C SER G 4 " pdb=" N LYS G 5 " ideal model delta sigma weight residual 116.20 126.31 -10.11 2.00e+00 2.50e-01 2.56e+01 angle pdb=" C TRP G 1 " pdb=" N ASN G 2 " pdb=" CA ASN G 2 " ideal model delta sigma weight residual 121.70 130.18 -8.48 1.80e+00 3.09e-01 2.22e+01 ... (remaining 42079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9926 17.80 - 35.61: 868 35.61 - 53.41: 244 53.41 - 71.21: 46 71.21 - 89.01: 9 Dihedral angle restraints: 11093 sinusoidal: 5971 harmonic: 5122 Sorted by residual: dihedral pdb=" C UX8 G 3 " pdb=" N UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " ideal model delta harmonic sigma weight residual -122.60 -138.22 15.62 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " ideal model delta harmonic sigma weight residual 122.80 137.89 -15.09 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" CA LEU A 699 " pdb=" C LEU A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual -180.00 -154.15 -25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 11090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1777 0.154 - 0.308: 1 0.308 - 0.462: 0 0.462 - 0.616: 1 0.616 - 0.770: 1 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CB UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CG UX8 G 3 " pdb=" O9 UX8 G 3 " both_signs ideal model delta sigma weight residual False -2.38 -3.15 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CA TRP G 1 " pdb=" N TRP G 1 " pdb=" C TRP G 1 " pdb=" CB TRP G 1 " both_signs ideal model delta sigma weight residual False 2.57 2.33 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1777 not shown) Planarity restraints: 3589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 1 " -0.066 2.00e-02 2.50e+03 4.35e-02 7.10e+01 pdb=" CG TRP G 1 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP G 1 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP G 1 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP G 1 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP G 1 " 0.109 2.00e-02 2.50e+03 pdb=" CE3 TRP G 1 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 1 " -0.099 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 1 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 1 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP G 1 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP G 1 " -0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP G 1 " 0.007 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 1 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP G 1 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 4 " -0.013 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C SER G 4 " 0.039 2.00e-02 2.50e+03 pdb=" O SER G 4 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS G 5 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 4 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" N LYS G 5 " -0.033 2.00e-02 2.50e+03 pdb=" CA LYS G 5 " 0.009 2.00e-02 2.50e+03 pdb=" H LYS G 5 " 0.014 2.00e-02 2.50e+03 ... (remaining 3586 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 952 2.17 - 2.78: 45005 2.78 - 3.39: 57865 3.39 - 3.99: 79739 3.99 - 4.60: 125234 Nonbonded interactions: 308795 Sorted by model distance: nonbonded pdb=" O ALA A 672 " pdb=" HG SER A 702 " model vdw 1.566 1.850 nonbonded pdb=" OD1 ASP B 384 " pdb=" HG1 THR B 386 " model vdw 1.570 1.850 nonbonded pdb=" HE ARG A 767 " pdb=" OD2 ASP A 797 " model vdw 1.598 1.850 nonbonded pdb=" OD1 ASN B 350 " pdb=" H VAL B 351 " model vdw 1.625 1.850 nonbonded pdb=" HZ1 LYS A 146 " pdb=" OG SER A 174 " model vdw 1.632 1.850 ... (remaining 308790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 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: 0.320 Extract box with map and model: 16.960 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 74.530 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.007 0.129 12051 Z= 0.467 Angle : 0.635 16.395 16378 Z= 0.348 Chirality : 0.049 0.770 1780 Planarity : 0.004 0.053 2156 Dihedral : 14.467 89.014 4360 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 0.32 % Allowed : 8.87 % Favored : 90.81 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: -3.46 (0.18), residues: 1486 helix: -1.26 (0.26), residues: 314 sheet: -1.84 (0.21), residues: 443 loop : -3.09 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.003 TRP G 1 HIS 0.004 0.001 HIS A 533 PHE 0.014 0.001 PHE A 791 TYR 0.014 0.001 TYR A 509 ARG 0.002 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7200 (m-30) cc_final: 0.6783 (m-30) outliers start: 4 outliers final: 3 residues processed: 164 average time/residue: 0.6791 time to fit residues: 149.7532 Evaluate side-chains 102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 538 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12051 Z= 0.193 Angle : 0.485 8.080 16378 Z= 0.256 Chirality : 0.043 0.140 1780 Planarity : 0.003 0.038 2156 Dihedral : 4.328 28.944 1653 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.71 % Allowed : 11.73 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.20), residues: 1486 helix: 0.01 (0.29), residues: 319 sheet: -1.41 (0.21), residues: 457 loop : -2.59 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.003 0.001 HIS A 533 PHE 0.007 0.001 PHE A 426 TYR 0.014 0.001 TYR D 184 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7264 (m-30) cc_final: 0.6809 (m-30) REVERT: A 500 ASP cc_start: 0.6487 (t0) cc_final: 0.6267 (t0) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.5401 time to fit residues: 81.6198 Evaluate side-chains 98 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12051 Z= 0.195 Angle : 0.458 5.541 16378 Z= 0.243 Chirality : 0.042 0.135 1780 Planarity : 0.003 0.038 2156 Dihedral : 4.101 20.911 1652 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.87 % Allowed : 12.84 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.80 (0.21), residues: 1486 helix: 0.71 (0.30), residues: 320 sheet: -1.05 (0.22), residues: 463 loop : -2.22 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS E 83 PHE 0.008 0.001 PHE A 426 TYR 0.013 0.001 TYR D 184 ARG 0.001 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7302 (m-30) cc_final: 0.6832 (m-30) REVERT: D 134 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7093 (m-30) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.5277 time to fit residues: 80.7148 Evaluate side-chains 95 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12051 Z= 0.241 Angle : 0.485 7.192 16378 Z= 0.258 Chirality : 0.043 0.148 1780 Planarity : 0.003 0.042 2156 Dihedral : 4.184 25.796 1650 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.11 % Allowed : 13.79 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.21), residues: 1486 helix: 1.14 (0.30), residues: 322 sheet: -0.81 (0.22), residues: 468 loop : -1.89 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.012 0.001 PHE A 791 TYR 0.014 0.001 TYR D 184 ARG 0.013 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7412 (m-30) cc_final: 0.7036 (m-30) REVERT: B 270 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8435 (mt) REVERT: D 134 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7040 (m-30) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.5153 time to fit residues: 77.0123 Evaluate side-chains 91 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12051 Z= 0.293 Angle : 0.488 6.487 16378 Z= 0.262 Chirality : 0.043 0.139 1780 Planarity : 0.003 0.044 2156 Dihedral : 4.272 27.031 1650 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.35 % Allowed : 13.87 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.21), residues: 1486 helix: 1.25 (0.30), residues: 322 sheet: -0.68 (0.22), residues: 466 loop : -1.82 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.012 0.001 PHE A 791 TYR 0.013 0.001 TYR C 41 ARG 0.002 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7487 (m-30) cc_final: 0.7019 (m-30) REVERT: D 134 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6981 (m-30) outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.5118 time to fit residues: 77.1950 Evaluate side-chains 94 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12051 Z= 0.182 Angle : 0.449 5.462 16378 Z= 0.239 Chirality : 0.042 0.133 1780 Planarity : 0.003 0.043 2156 Dihedral : 4.106 26.383 1650 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.11 % Allowed : 13.71 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.22), residues: 1486 helix: 1.52 (0.30), residues: 321 sheet: -0.50 (0.23), residues: 465 loop : -1.69 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 PHE 0.007 0.001 PHE A 791 TYR 0.014 0.001 TYR D 184 ARG 0.001 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7455 (m-30) cc_final: 0.6965 (m-30) REVERT: D 134 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6967 (m-30) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.5136 time to fit residues: 72.4164 Evaluate side-chains 91 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12051 Z= 0.241 Angle : 0.461 5.611 16378 Z= 0.247 Chirality : 0.042 0.135 1780 Planarity : 0.003 0.045 2156 Dihedral : 4.127 23.922 1650 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.43 % Allowed : 13.79 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.21), residues: 1486 helix: 1.57 (0.29), residues: 323 sheet: -0.49 (0.23), residues: 471 loop : -1.64 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.003 0.001 HIS D 102 PHE 0.010 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.002 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7479 (m-30) cc_final: 0.7003 (m-30) REVERT: D 134 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6929 (m-30) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.4946 time to fit residues: 71.8690 Evaluate side-chains 97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12051 Z= 0.301 Angle : 0.493 5.811 16378 Z= 0.266 Chirality : 0.043 0.144 1780 Planarity : 0.004 0.041 2156 Dihedral : 4.342 23.758 1650 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.66 % Allowed : 13.87 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.21), residues: 1486 helix: 1.63 (0.29), residues: 322 sheet: -0.50 (0.23), residues: 480 loop : -1.66 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 546 HIS 0.003 0.001 HIS D 102 PHE 0.013 0.001 PHE A 791 TYR 0.015 0.001 TYR C 41 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7555 (m-30) cc_final: 0.7097 (m-30) outliers start: 21 outliers final: 16 residues processed: 101 average time/residue: 0.5173 time to fit residues: 76.8268 Evaluate side-chains 97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN D 40 GLN D 102 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12051 Z= 0.144 Angle : 0.445 5.305 16378 Z= 0.239 Chirality : 0.042 0.134 1780 Planarity : 0.003 0.041 2156 Dihedral : 4.108 23.717 1650 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.11 % Allowed : 14.58 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1486 helix: 1.92 (0.29), residues: 323 sheet: -0.26 (0.23), residues: 461 loop : -1.52 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 546 HIS 0.005 0.001 HIS D 102 PHE 0.007 0.001 PHE A 791 TYR 0.014 0.001 TYR D 184 ARG 0.001 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7487 (m-30) cc_final: 0.7003 (m-30) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 0.5050 time to fit residues: 71.2140 Evaluate side-chains 93 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12051 Z= 0.229 Angle : 0.460 5.469 16378 Z= 0.246 Chirality : 0.042 0.136 1780 Planarity : 0.003 0.044 2156 Dihedral : 4.117 22.431 1650 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.03 % Allowed : 14.66 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1486 helix: 1.98 (0.29), residues: 321 sheet: -0.35 (0.23), residues: 480 loop : -1.48 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 546 HIS 0.002 0.001 HIS A 533 PHE 0.009 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.006 0.000 ARG A 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7507 (m-30) cc_final: 0.7024 (m-30) outliers start: 13 outliers final: 13 residues processed: 95 average time/residue: 0.5274 time to fit residues: 73.7908 Evaluate side-chains 94 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072183 restraints weight = 66174.426| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12051 Z= 0.191 Angle : 0.446 5.168 16378 Z= 0.239 Chirality : 0.042 0.134 1780 Planarity : 0.003 0.042 2156 Dihedral : 4.049 22.606 1650 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.95 % Allowed : 15.06 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.22), residues: 1486 helix: 2.12 (0.29), residues: 323 sheet: -0.23 (0.23), residues: 470 loop : -1.43 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 546 HIS 0.002 0.000 HIS A 533 PHE 0.008 0.001 PHE A 791 TYR 0.013 0.001 TYR D 184 ARG 0.004 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5134.99 seconds wall clock time: 91 minutes 39.48 seconds (5499.48 seconds total)