Starting phenix.real_space_refine on Mon Mar 18 08:35:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/03_2024/8pt6_17868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/03_2024/8pt6_17868.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/8pt6_17868/03_2024/8pt6_17868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/03_2024/8pt6_17868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/03_2024/8pt6_17868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/03_2024/8pt6_17868_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= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 31 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6433 2.51 5 N 1828 2.21 5 O 2025 1.98 5 H 10051 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Conformer: "B" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} bond proxies already assigned to first conformer: 8041 Chain: "C" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4887 Classifications: {'peptide': 310} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 1 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 44.562 50.821 17.982 1.00 61.93 S ATOM 4473 SG CYS A 282 42.322 48.732 15.482 1.00 64.89 S ATOM 16942 SG CYS C 146 29.762 69.730 80.614 1.00127.37 S ATOM 17130 SG CYS C 159 31.471 69.008 77.299 1.00111.13 S ATOM 17185 SG CYS C 163 32.787 71.906 79.371 1.00119.08 S ATOM 17195 SG CYS C 164 33.107 68.366 80.746 1.00108.45 S ATOM 18275 SG CYS C 233 36.504 91.333 70.828 1.00139.04 S ATOM 18300 SG CYS C 235 37.665 88.886 73.425 1.00130.85 S Time building chain proxies: 13.44, per 1000 atoms: 0.66 Number of scatterers: 20436 At special positions: 0 Unit cell: (89.04, 114.24, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 31 15.00 Mg 2 11.99 O 2025 8.00 N 1828 7.00 C 6433 6.00 H 10051 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.29 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 164 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 235 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 233 " Number of angles added : 8 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 35.3% alpha, 11.0% beta 7 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 10.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 4.599A pdb=" N GLN A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 9 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.627A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.690A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.242A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.708A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 182 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 217 through 220 No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.849A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.925A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 454 removed outlier: 3.673A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.553A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 removed outlier: 5.737A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 88 through 97 Processing helix chain 'C' and resid 101 through 108 removed outlier: 3.584A pdb=" N LEU C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 151 No H-bonds generated for 'chain 'C' and resid 148 through 151' Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 235 through 240 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.529A pdb=" N VAL A 69 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU A 56 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS A 71 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.329A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 74 through 80 Processing sheet with id= D, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.666A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 321 through 323 Processing sheet with id= F, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 83 Processing sheet with id= H, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.856A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.665A pdb=" N VAL C 221 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER C 203 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS C 223 " --> pdb=" O SER C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 406 through 409 removed outlier: 3.795A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 17.93 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: 10019 1.03 - 1.23: 44 1.23 - 1.42: 4497 1.42 - 1.62: 6061 1.62 - 1.81: 87 Bond restraints: 20708 Sorted by residual: bond pdb=" C5 CTP F 1 " pdb=" C6 CTP F 1 " ideal model delta sigma weight residual 1.390 1.342 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C4' CTP F 1 " pdb=" O4' CTP F 1 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C5' CTP F 1 " pdb=" O5' CTP F 1 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C4 CTP F 1 " pdb=" N3 CTP F 1 " ideal model delta sigma weight residual 1.380 1.340 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 CTP F 1 " pdb=" C5 CTP F 1 " ideal model delta sigma weight residual 1.390 1.421 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.73: 456 106.73 - 113.68: 24449 113.68 - 120.62: 7208 120.62 - 127.57: 5139 127.57 - 134.52: 145 Bond angle restraints: 37397 Sorted by residual: angle pdb=" PA CTP F 1 " pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sigma weight residual 120.50 134.52 -14.02 3.00e+00 1.11e-01 2.19e+01 angle pdb=" PB CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sigma weight residual 120.50 131.79 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C2' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" C4' CTP F 1 " ideal model delta sigma weight residual 111.00 99.78 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C1' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" C3' CTP F 1 " ideal model delta sigma weight residual 111.00 99.91 11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O1B CTP F 1 " pdb=" PB CTP F 1 " pdb=" O2B CTP F 1 " ideal model delta sigma weight residual 109.50 119.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 37392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 9343 35.28 - 70.56: 413 70.56 - 105.84: 19 105.84 - 141.11: 1 141.11 - 176.39: 2 Dihedral angle restraints: 9778 sinusoidal: 5559 harmonic: 4219 Sorted by residual: dihedral pdb=" O3B CTP F 1 " pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " pdb=" PA CTP F 1 " ideal model delta sinusoidal sigma weight residual 320.71 166.48 154.22 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1G CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sinusoidal sigma weight residual 82.72 -169.86 -107.42 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" O3A CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PB CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sinusoidal sigma weight residual -155.50 -52.04 -103.46 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 9775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1440 0.051 - 0.102: 154 0.102 - 0.153: 40 0.153 - 0.204: 0 0.204 - 0.255: 1 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C2' CTP F 1 " pdb=" C1' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" O2' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" C3' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" C4' CTP F 1 " pdb=" O3' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.61 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1632 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 162 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 8 " 0.019 2.00e-02 2.50e+03 8.45e-03 2.32e+00 pdb=" N9 A S 8 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A S 8 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A S 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A S 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A S 8 " 0.000 2.00e-02 2.50e+03 pdb=" H8 A S 8 " -0.000 2.00e-02 2.50e+03 pdb=" H2 A S 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO B 470 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.019 5.00e-02 4.00e+02 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.72: 25 1.72 - 2.44: 11323 2.44 - 3.16: 62222 3.16 - 3.88: 84236 3.88 - 4.60: 134040 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291846 Sorted by model distance: nonbonded pdb=" HD2 HIS C 266 " pdb="HG13 VAL C 269 " model vdw 0.997 2.270 nonbonded pdb=" HB2 CYS C 233 " pdb="ZN ZN C 502 " model vdw 1.374 1.544 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.484 1.850 nonbonded pdb=" O GLY A 309 " pdb="HH22 ARG B 394 " model vdw 1.559 1.850 nonbonded pdb=" OD2 ASP A 43 " pdb=" H PHE A 55 " model vdw 1.574 1.850 ... (remaining 291841 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.240 Extract box with map and model: 6.200 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 85.690 Find NCS groups from input model: 0.340 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.003 0.048 10657 Z= 0.162 Angle : 0.546 14.024 14537 Z= 0.270 Chirality : 0.037 0.255 1635 Planarity : 0.003 0.051 1766 Dihedral : 18.464 176.392 4163 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 25.02 % Favored : 72.55 % 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: 1.06 (0.25), residues: 1234 helix: 1.99 (0.25), residues: 477 sheet: 0.43 (0.42), residues: 150 loop : -0.22 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 183 HIS 0.002 0.001 HIS A 371 PHE 0.010 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.005 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 219 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7781 (mp0) outliers start: 26 outliers final: 23 residues processed: 115 average time/residue: 0.5792 time to fit residues: 90.6318 Evaluate side-chains 112 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8455 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10657 Z= 0.254 Angle : 0.504 6.199 14537 Z= 0.258 Chirality : 0.038 0.163 1635 Planarity : 0.004 0.054 1766 Dihedral : 13.470 175.657 1829 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 3.17 % Allowed : 23.16 % Favored : 73.67 % 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: 0.88 (0.24), residues: 1234 helix: 1.82 (0.25), residues: 472 sheet: 0.25 (0.41), residues: 148 loop : -0.27 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS C 22 PHE 0.016 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8566 (mp) REVERT: B 219 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8064 (mt-10) outliers start: 34 outliers final: 21 residues processed: 113 average time/residue: 0.5696 time to fit residues: 88.0478 Evaluate side-chains 109 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10657 Z= 0.280 Angle : 0.510 5.944 14537 Z= 0.263 Chirality : 0.039 0.141 1635 Planarity : 0.004 0.053 1766 Dihedral : 13.338 173.268 1808 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 2.71 % Allowed : 23.34 % Favored : 73.95 % 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 (0.24), residues: 1234 helix: 1.68 (0.24), residues: 471 sheet: 0.18 (0.41), residues: 148 loop : -0.39 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS C 22 PHE 0.016 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8390 (mppt) REVERT: A 148 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: B 219 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 50 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7528 (tm-30) outliers start: 29 outliers final: 18 residues processed: 111 average time/residue: 0.6487 time to fit residues: 95.1276 Evaluate side-chains 105 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10657 Z= 0.226 Angle : 0.487 5.745 14537 Z= 0.249 Chirality : 0.038 0.139 1635 Planarity : 0.004 0.052 1766 Dihedral : 13.137 174.921 1803 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 3.55 % Allowed : 22.41 % Favored : 74.04 % 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: 0.77 (0.24), residues: 1234 helix: 1.77 (0.25), residues: 471 sheet: 0.35 (0.42), residues: 144 loop : -0.41 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 83 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8385 (mppt) REVERT: B 121 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 219 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: B 264 MET cc_start: 0.8943 (ptt) cc_final: 0.8685 (ptt) REVERT: C 50 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7485 (tm-30) outliers start: 38 outliers final: 26 residues processed: 112 average time/residue: 0.5542 time to fit residues: 86.5309 Evaluate side-chains 113 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10657 Z= 0.251 Angle : 0.493 5.760 14537 Z= 0.254 Chirality : 0.038 0.137 1635 Planarity : 0.004 0.052 1766 Dihedral : 13.186 174.324 1801 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 3.27 % Allowed : 22.13 % Favored : 74.60 % 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: 0.72 (0.24), residues: 1234 helix: 1.73 (0.25), residues: 471 sheet: 0.33 (0.42), residues: 144 loop : -0.44 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.016 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 83 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8439 (mppt) REVERT: A 317 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7926 (ttm170) REVERT: B 121 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 219 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: C 50 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: C 185 MET cc_start: 0.4586 (mtm) cc_final: 0.4373 (mtm) outliers start: 35 outliers final: 26 residues processed: 108 average time/residue: 0.6118 time to fit residues: 88.9336 Evaluate side-chains 114 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8491 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10657 Z= 0.311 Angle : 0.518 5.690 14537 Z= 0.268 Chirality : 0.039 0.148 1635 Planarity : 0.004 0.053 1766 Dihedral : 13.328 173.949 1800 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 4.01 % Allowed : 21.66 % Favored : 74.32 % 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: 0.56 (0.24), residues: 1234 helix: 1.58 (0.24), residues: 471 sheet: 0.29 (0.42), residues: 144 loop : -0.53 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.018 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 83 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8450 (mppt) REVERT: A 148 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: B 121 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (mp) REVERT: B 124 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7960 (mtpp) REVERT: B 219 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: B 264 MET cc_start: 0.8981 (ptt) cc_final: 0.8690 (ptt) REVERT: C 50 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7492 (tm-30) outliers start: 43 outliers final: 30 residues processed: 117 average time/residue: 0.5981 time to fit residues: 95.2757 Evaluate side-chains 118 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10657 Z= 0.168 Angle : 0.468 5.790 14537 Z= 0.239 Chirality : 0.037 0.138 1635 Planarity : 0.004 0.050 1766 Dihedral : 13.153 174.781 1800 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.61 % Allowed : 22.50 % Favored : 74.88 % 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: 0.77 (0.24), residues: 1234 helix: 1.84 (0.25), residues: 471 sheet: 0.19 (0.42), residues: 149 loop : -0.43 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.002 0.001 HIS B 174 PHE 0.013 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8422 (mppt) REVERT: A 317 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7903 (ttm170) REVERT: C 50 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7506 (tm-30) outliers start: 28 outliers final: 24 residues processed: 105 average time/residue: 0.6211 time to fit residues: 87.8086 Evaluate side-chains 109 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10657 Z= 0.253 Angle : 0.491 5.705 14537 Z= 0.253 Chirality : 0.038 0.141 1635 Planarity : 0.004 0.052 1766 Dihedral : 13.151 176.847 1797 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 3.27 % Allowed : 21.76 % Favored : 74.98 % 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 (0.24), residues: 1234 helix: 1.71 (0.25), residues: 471 sheet: 0.14 (0.43), residues: 149 loop : -0.47 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.016 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8457 (mppt) REVERT: A 317 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: C 50 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7514 (tm-30) outliers start: 35 outliers final: 28 residues processed: 115 average time/residue: 0.6170 time to fit residues: 96.4004 Evaluate side-chains 115 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10657 Z= 0.250 Angle : 0.493 5.739 14537 Z= 0.254 Chirality : 0.038 0.137 1635 Planarity : 0.004 0.052 1766 Dihedral : 13.022 174.174 1797 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 3.36 % Allowed : 21.85 % Favored : 74.79 % 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: 0.62 (0.24), residues: 1234 helix: 1.68 (0.25), residues: 470 sheet: 0.06 (0.42), residues: 149 loop : -0.47 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8452 (mppt) REVERT: A 317 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: C 50 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7509 (tm-30) outliers start: 36 outliers final: 31 residues processed: 117 average time/residue: 0.6121 time to fit residues: 96.5244 Evaluate side-chains 119 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 85 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10657 Z= 0.136 Angle : 0.457 5.984 14537 Z= 0.232 Chirality : 0.036 0.139 1635 Planarity : 0.003 0.050 1766 Dihedral : 12.505 174.950 1797 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.15 % Allowed : 23.16 % Favored : 74.70 % 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: 0.88 (0.24), residues: 1234 helix: 1.94 (0.25), residues: 471 sheet: 0.15 (0.42), residues: 149 loop : -0.34 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 183 HIS 0.002 0.000 HIS C 191 PHE 0.010 0.001 PHE C 44 TYR 0.007 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8407 (mppt) REVERT: A 317 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: C 50 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7508 (tm-30) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.6394 time to fit residues: 92.6621 Evaluate side-chains 106 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.148145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103299 restraints weight = 41302.663| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.36 r_work: 0.3044 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10657 Z= 0.138 Angle : 0.449 5.902 14537 Z= 0.228 Chirality : 0.036 0.138 1635 Planarity : 0.003 0.050 1766 Dihedral : 12.052 174.932 1797 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.05 % Allowed : 23.06 % Favored : 74.88 % 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: 1.00 (0.25), residues: 1234 helix: 2.03 (0.25), residues: 471 sheet: 0.19 (0.42), residues: 149 loop : -0.25 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 2 HIS 0.002 0.001 HIS C 191 PHE 0.011 0.001 PHE C 44 TYR 0.007 0.001 TYR A 403 ARG 0.002 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4844.16 seconds wall clock time: 86 minutes 52.30 seconds (5212.30 seconds total)