Starting phenix.real_space_refine (version: dev) on Wed Dec 14 23:19:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/12_2022/7nri_12546_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/12_2022/7nri_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_12546/12_2022/7nri_12546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/12_2022/7nri_12546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/12_2022/7nri_12546_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nri_12546/12_2022/7nri_12546_trim_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 11.58, per 1000 atoms: 0.50 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: 18.86 Conformation dependent library (CDL) restraints added in 2.0 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: 1.66 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: 8.69 Time building geometry restraints manager: 19.63 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: 8520 17.80 - 35.61: 726 35.61 - 53.41: 136 53.41 - 71.21: 22 71.21 - 89.01: 9 Dihedral angle restraints: 9413 sinusoidal: 4291 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 9410 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 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. 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: 5.070 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: 0.360 Extract box with map and model: 17.170 Check model and map are aligned: 0.390 Convert atoms to be neutral: 0.220 Process input model: 72.790 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 % 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 *********************** 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 : 2.033 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 outliers start: 4 outliers final: 3 residues processed: 164 average time/residue: 0.6133 time to fit residues: 138.3754 Evaluate side-chains 102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2410 time to fit residues: 3.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 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: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12051 Z= 0.179 Angle : 0.487 8.006 16378 Z= 0.256 Chirality : 0.042 0.140 1780 Planarity : 0.003 0.038 2156 Dihedral : 4.201 25.146 1649 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.40 % 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: -2.35 (0.20), residues: 1486 helix: 0.13 (0.29), residues: 319 sheet: -1.33 (0.21), residues: 455 loop : -2.54 (0.20), residues: 712 *********************** 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 104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.4903 time to fit residues: 72.6020 Evaluate side-chains 94 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 2.031 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2794 time to fit residues: 3.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 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: 2.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 12051 Z= 0.268 Angle : 0.495 5.959 16378 Z= 0.263 Chirality : 0.043 0.140 1780 Planarity : 0.003 0.041 2156 Dihedral : 4.197 21.360 1649 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.87 % 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: -1.75 (0.21), residues: 1486 helix: 0.71 (0.30), residues: 321 sheet: -1.05 (0.22), residues: 465 loop : -2.16 (0.22), residues: 700 *********************** 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 104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.5058 time to fit residues: 74.6531 Evaluate side-chains 88 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 2.080 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2630 time to fit residues: 5.2391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2498 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= 0.203 Angle : 0.462 5.622 16378 Z= 0.245 Chirality : 0.042 0.132 1780 Planarity : 0.003 0.040 2156 Dihedral : 4.094 23.460 1649 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.55 % 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: -1.30 (0.21), residues: 1486 helix: 1.12 (0.30), residues: 322 sheet: -0.77 (0.22), residues: 464 loop : -1.90 (0.22), residues: 700 *********************** 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 95 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.5052 time to fit residues: 69.4432 Evaluate side-chains 84 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.847 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.4628 time to fit residues: 4.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.8547 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 12051 Z= 0.245 Angle : 0.474 5.845 16378 Z= 0.253 Chirality : 0.042 0.138 1780 Planarity : 0.003 0.041 2156 Dihedral : 4.135 24.757 1649 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.40 % 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: -1.12 (0.21), residues: 1486 helix: 1.28 (0.30), residues: 322 sheet: -0.67 (0.23), residues: 464 loop : -1.78 (0.23), residues: 700 *********************** 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 89 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 0.5052 time to fit residues: 65.6969 Evaluate side-chains 82 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.902 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2711 time to fit residues: 4.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8532 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12051 Z= 0.175 Angle : 0.451 5.808 16378 Z= 0.240 Chirality : 0.042 0.133 1780 Planarity : 0.003 0.040 2156 Dihedral : 4.053 28.842 1649 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.32 % 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: 1.56 (0.30), residues: 321 sheet: -0.54 (0.23), residues: 467 loop : -1.69 (0.23), residues: 698 *********************** 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 88 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.4513 time to fit residues: 59.9115 Evaluate side-chains 77 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.904 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3273 time to fit residues: 3.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8530 moved from start: 0.3061 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= 0.176 Angle : 0.446 5.277 16378 Z= 0.236 Chirality : 0.042 0.133 1780 Planarity : 0.003 0.039 2156 Dihedral : 3.945 24.369 1649 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.24 % 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: -0.70 (0.22), residues: 1486 helix: 1.75 (0.29), residues: 321 sheet: -0.45 (0.23), residues: 471 loop : -1.56 (0.23), residues: 694 *********************** 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 83 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.4904 time to fit residues: 63.0190 Evaluate side-chains 78 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.899 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4105 time to fit residues: 3.0210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 D 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 12051 Z= 0.382 Angle : 0.525 6.106 16378 Z= 0.282 Chirality : 0.044 0.153 1780 Planarity : 0.003 0.040 2156 Dihedral : 4.329 25.054 1649 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.71 % 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: -0.92 (0.21), residues: 1486 helix: 1.55 (0.29), residues: 322 sheet: -0.53 (0.23), residues: 474 loop : -1.73 (0.22), residues: 690 *********************** 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 89 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.4571 time to fit residues: 60.8115 Evaluate side-chains 84 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2288 time to fit residues: 4.8658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 12051 Z= 0.179 Angle : 0.458 5.443 16378 Z= 0.243 Chirality : 0.042 0.136 1780 Planarity : 0.003 0.037 2156 Dihedral : 4.130 25.619 1649 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % 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: -0.66 (0.22), residues: 1486 helix: 1.83 (0.29), residues: 320 sheet: -0.36 (0.23), residues: 468 loop : -1.61 (0.23), residues: 698 *********************** 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 82 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4945 time to fit residues: 62.4503 Evaluate side-chains 79 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 12051 Z= 0.311 Angle : 0.498 5.845 16378 Z= 0.266 Chirality : 0.043 0.147 1780 Planarity : 0.003 0.035 2156 Dihedral : 4.251 24.286 1649 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.16 % 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: -0.74 (0.22), residues: 1486 helix: 1.73 (0.29), residues: 322 sheet: -0.42 (0.23), residues: 480 loop : -1.65 (0.23), residues: 684 ********************** 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 80 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.5120 time to fit residues: 62.0782 Evaluate side-chains 77 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 107 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 116 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073090 restraints weight = 65637.603| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.39 r_work: 0.3059 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12051 Z= 0.116 Angle : 0.439 4.996 16378 Z= 0.233 Chirality : 0.042 0.136 1780 Planarity : 0.003 0.038 2156 Dihedral : 3.971 24.923 1649 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % 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: -0.37 (0.22), residues: 1486 helix: 2.13 (0.29), residues: 322 sheet: -0.18 (0.23), residues: 471 loop : -1.46 (0.23), residues: 693 =============================================================================== Job complete usr+sys time: 4795.73 seconds wall clock time: 85 minutes 37.27 seconds (5137.27 seconds total)