Starting phenix.real_space_refine on Sun Mar 17 13:08:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptj_17872/03_2024/8ptj_17872.pdb" } resolution = 2.86 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 18 5.49 5 S 54 5.16 5 C 5616 2.51 5 N 1587 2.21 5 O 1757 1.98 5 H 8841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 396": "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: 17874 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7862 Classifications: {'peptide': 511} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain breaks: 1 Chain: "C" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2792 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Chain: "D" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 192 Classifications: {'RNA': 6} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Conformer: "B" Number of residues, atoms: 6, 192 Classifications: {'RNA': 6} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 3} bond proxies already assigned to first conformer: 106 Chain: "V" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 3} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 45.530 46.138 18.978 1.00 67.01 S ATOM 4472 SG CYS A 282 43.431 44.368 16.160 1.00 66.74 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A A D 12 " occ=0.60 ... (64 atoms not shown) pdb=" H2 B A D 12 " occ=0.40 residue: pdb=" P A U D 13 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 13 " occ=0.40 residue: pdb=" P A U D 14 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 14 " occ=0.40 Time building chain proxies: 8.90, per 1000 atoms: 0.50 Number of scatterers: 17874 At special positions: 0 Unit cell: (88.2, 87.36, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 18 15.00 O 1757 8.00 N 1587 7.00 C 5616 6.00 H 8841 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: 15.27 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 2 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 45.0% alpha, 12.3% beta 2 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.931A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.719A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.395A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.866A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.669A pdb=" N TYR A 386 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.617A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.713A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.769A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.651A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.824A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.562A pdb=" N SER B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.589A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.999A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 455 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.387A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.592A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.592A pdb=" N TRP A 198 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN A 200 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.083A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 385 through 388 removed outlier: 6.501A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 15.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 8811 1.05 - 1.25: 1477 1.25 - 1.46: 3622 1.46 - 1.67: 4094 1.67 - 1.88: 77 Bond restraints: 18081 Sorted by residual: bond pdb=" O3'B U D 14 " pdb=" P U D 15 " ideal model delta sigma weight residual 1.607 1.879 -0.272 1.50e-02 4.44e+03 3.28e+02 bond pdb=" N GLN C 88 " pdb=" CA GLN C 88 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.74e+00 bond pdb=" N ILE C 92 " pdb=" CA ILE C 92 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N THR C 87 " pdb=" H THR C 87 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.32e+00 ... (remaining 18076 not shown) Histogram of bond angle deviations from ideal: 96.29 - 103.83: 161 103.83 - 111.37: 20153 111.37 - 118.91: 4712 118.91 - 126.45: 7457 126.45 - 133.99: 168 Bond angle restraints: 32651 Sorted by residual: angle pdb=" O3'B U D 14 " pdb=" P U D 15 " pdb=" O5' U D 15 " ideal model delta sigma weight residual 104.00 96.29 7.71 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C3'B U D 14 " pdb=" O3'B U D 14 " pdb=" P U D 15 " ideal model delta sigma weight residual 120.20 126.06 -5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" O THR C 87 " ideal model delta sigma weight residual 121.81 117.61 4.20 1.18e+00 7.18e-01 1.27e+01 angle pdb=" C GLU C 90 " pdb=" N ALA C 91 " pdb=" CA ALA C 91 " ideal model delta sigma weight residual 120.54 125.25 -4.71 1.35e+00 5.49e-01 1.22e+01 angle pdb=" C GLN C 88 " pdb=" N GLU C 89 " pdb=" CA GLU C 89 " ideal model delta sigma weight residual 120.54 125.19 -4.65 1.35e+00 5.49e-01 1.18e+01 ... (remaining 32646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7491 17.80 - 35.60: 678 35.60 - 53.39: 267 53.39 - 71.19: 72 71.19 - 88.99: 20 Dihedral angle restraints: 8528 sinusoidal: 4821 harmonic: 3707 Sorted by residual: dihedral pdb=" CA SER A 19 " pdb=" C SER A 19 " pdb=" N GLU A 20 " pdb=" CA GLU A 20 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP B 213 " pdb=" CB ASP B 213 " pdb=" CG ASP B 213 " pdb=" OD1 ASP B 213 " ideal model delta sinusoidal sigma weight residual -30.00 -86.21 56.21 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE1 GLU B 29 " ideal model delta sinusoidal sigma weight residual 0.00 88.51 -88.51 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1008 0.032 - 0.063: 298 0.063 - 0.095: 68 0.095 - 0.126: 50 0.126 - 0.158: 3 Chirality restraints: 1427 Sorted by residual: chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA LEU C 86 " pdb=" N LEU C 86 " pdb=" C LEU C 86 " pdb=" CB LEU C 86 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1424 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " -0.203 9.50e-02 1.11e+02 6.80e-02 5.70e+00 pdb=" NE ARG A 34 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 34 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 34 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 34 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 34 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 217 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 218 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.019 2.00e-02 2.50e+03 7.50e-03 1.83e+00 pdb=" N9 A V 4 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.001 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 538 2.14 - 2.76: 33099 2.76 - 3.37: 50583 3.37 - 3.99: 66482 3.99 - 4.60: 103404 Nonbonded interactions: 254106 Sorted by model distance: nonbonded pdb="HG21 THR A 236 " pdb=" OP1B U D 13 " model vdw 1.529 2.620 nonbonded pdb=" OE1 GLU B 119 " pdb=" H GLU B 119 " model vdw 1.532 1.850 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.592 1.850 nonbonded pdb=" OE1 GLU B 381 " pdb=" H PHE B 420 " model vdw 1.620 1.850 nonbonded pdb=" O PHE A 55 " pdb="HH11 ARG A 62 " model vdw 1.642 1.850 ... (remaining 254101 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=0.99 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: 1.630 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: 0.250 Extract box with map and model: 8.210 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 72.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 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 : 0.004 0.272 9240 Z= 0.221 Angle : 0.485 7.708 12559 Z= 0.273 Chirality : 0.036 0.158 1427 Planarity : 0.004 0.089 1550 Dihedral : 17.879 88.990 3586 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 20.38 % Favored : 76.80 % 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: 1.19 (0.27), residues: 1090 helix: 2.18 (0.26), residues: 446 sheet: -0.21 (0.53), residues: 99 loop : -0.16 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.018 0.001 PHE B 407 TYR 0.008 0.001 TYR A 403 ARG 0.014 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.8886 (tt0) cc_final: 0.8686 (tt0) REVERT: C 89 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 93 ASP cc_start: 0.8323 (m-30) cc_final: 0.7928 (m-30) REVERT: C 113 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (t) outliers start: 27 outliers final: 23 residues processed: 124 average time/residue: 2.5052 time to fit residues: 333.1344 Evaluate side-chains 118 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8911 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9240 Z= 0.254 Angle : 0.478 5.100 12559 Z= 0.247 Chirality : 0.037 0.127 1427 Planarity : 0.004 0.043 1550 Dihedral : 10.837 73.581 1508 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.13 % Allowed : 19.75 % Favored : 77.12 % 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: 1.13 (0.26), residues: 1090 helix: 2.15 (0.25), residues: 451 sheet: -0.26 (0.51), residues: 107 loop : -0.23 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.020 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.430 Fit side-chains REVERT: A 34 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7345 (ttp-110) REVERT: A 323 ASP cc_start: 0.8564 (t0) cc_final: 0.8237 (t0) REVERT: A 326 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 497 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8315 (tp) REVERT: C 93 ASP cc_start: 0.8370 (m-30) cc_final: 0.8135 (m-30) REVERT: C 113 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8076 (t) outliers start: 30 outliers final: 14 residues processed: 118 average time/residue: 2.5815 time to fit residues: 325.9404 Evaluate side-chains 114 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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: 0.8891 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9240 Z= 0.153 Angle : 0.439 4.616 12559 Z= 0.227 Chirality : 0.036 0.127 1427 Planarity : 0.003 0.036 1550 Dihedral : 10.475 73.553 1493 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.61 % Allowed : 20.17 % Favored : 77.22 % 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: 1.25 (0.26), residues: 1090 helix: 2.30 (0.26), residues: 451 sheet: -0.21 (0.51), residues: 107 loop : -0.20 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.017 0.001 PHE B 407 TYR 0.008 0.001 TYR A 403 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8342 (t0) cc_final: 0.8036 (t0) REVERT: A 326 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 57 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: B 507 TYR cc_start: 0.8649 (t80) cc_final: 0.8398 (t80) REVERT: C 83 ARG cc_start: 0.8130 (mpp80) cc_final: 0.7873 (mpt180) REVERT: C 113 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8078 (t) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 2.5921 time to fit residues: 330.6918 Evaluate side-chains 116 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9240 Z= 0.196 Angle : 0.448 4.350 12559 Z= 0.233 Chirality : 0.036 0.127 1427 Planarity : 0.003 0.037 1550 Dihedral : 10.163 73.561 1488 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.72 % Allowed : 19.12 % Favored : 78.16 % 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: 1.23 (0.26), residues: 1090 helix: 2.30 (0.26), residues: 451 sheet: -0.25 (0.50), residues: 107 loop : -0.24 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.019 0.001 PHE B 407 TYR 0.009 0.001 TYR A 403 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.433 Fit side-chains REVERT: A 118 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: A 323 ASP cc_start: 0.8511 (t0) cc_final: 0.8165 (t0) REVERT: A 326 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 57 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: B 507 TYR cc_start: 0.8673 (t80) cc_final: 0.8426 (t80) REVERT: C 113 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7993 (t) outliers start: 26 outliers final: 16 residues processed: 118 average time/residue: 2.6114 time to fit residues: 329.7858 Evaluate side-chains 121 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9240 Z= 0.384 Angle : 0.525 5.582 12559 Z= 0.276 Chirality : 0.039 0.131 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.101 73.620 1481 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 3.66 % Allowed : 19.12 % Favored : 77.22 % 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 (0.26), residues: 1090 helix: 2.00 (0.25), residues: 451 sheet: -0.39 (0.51), residues: 105 loop : -0.39 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 426 HIS 0.006 0.001 HIS B 174 PHE 0.024 0.002 PHE B 407 TYR 0.011 0.001 TYR A 403 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7482 (ttp-110) REVERT: A 323 ASP cc_start: 0.8669 (t0) cc_final: 0.8265 (t0) REVERT: A 326 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: C 113 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8092 (t) outliers start: 35 outliers final: 23 residues processed: 123 average time/residue: 2.7507 time to fit residues: 361.3285 Evaluate side-chains 125 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9240 Z= 0.212 Angle : 0.468 5.402 12559 Z= 0.244 Chirality : 0.037 0.133 1427 Planarity : 0.004 0.038 1550 Dihedral : 10.009 73.580 1481 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.24 % Allowed : 19.54 % Favored : 77.22 % 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: 1.05 (0.26), residues: 1090 helix: 2.13 (0.25), residues: 451 sheet: -0.30 (0.51), residues: 105 loop : -0.33 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.020 0.001 PHE B 407 TYR 0.008 0.001 TYR A 18 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8515 (t0) cc_final: 0.8114 (t0) REVERT: A 326 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: B 507 TYR cc_start: 0.8672 (t80) cc_final: 0.8429 (t80) REVERT: C 90 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8174 (mt-10) REVERT: C 113 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8043 (t) outliers start: 31 outliers final: 20 residues processed: 122 average time/residue: 2.7586 time to fit residues: 359.8328 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 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 : 0.005 0.038 9240 Z= 0.336 Angle : 0.508 5.428 12559 Z= 0.266 Chirality : 0.038 0.132 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.085 73.612 1481 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 19.33 % Favored : 76.80 % 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 (0.26), residues: 1090 helix: 2.01 (0.25), residues: 451 sheet: -0.40 (0.54), residues: 93 loop : -0.41 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.023 0.001 PHE B 407 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7462 (ttp-110) REVERT: A 323 ASP cc_start: 0.8616 (t0) cc_final: 0.8198 (t0) REVERT: A 326 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: B 507 TYR cc_start: 0.8698 (t80) cc_final: 0.8449 (t80) REVERT: C 113 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (t) outliers start: 37 outliers final: 24 residues processed: 125 average time/residue: 2.6952 time to fit residues: 359.6241 Evaluate side-chains 123 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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: 0.8906 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9240 Z= 0.164 Angle : 0.456 5.768 12559 Z= 0.236 Chirality : 0.036 0.132 1427 Planarity : 0.004 0.046 1550 Dihedral : 9.980 73.569 1481 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.82 % Allowed : 20.38 % Favored : 76.80 % 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: 1.15 (0.26), residues: 1090 helix: 2.23 (0.26), residues: 451 sheet: -0.28 (0.50), residues: 105 loop : -0.28 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.019 0.001 PHE B 407 TYR 0.008 0.001 TYR A 403 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7444 (ttp-110) REVERT: A 323 ASP cc_start: 0.8437 (t0) cc_final: 0.8077 (t0) REVERT: A 326 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: B 467 ASP cc_start: 0.8346 (t0) cc_final: 0.8115 (t0) REVERT: B 507 TYR cc_start: 0.8643 (t80) cc_final: 0.8392 (t80) REVERT: C 111 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6993 (ttp-110) REVERT: C 113 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (t) outliers start: 27 outliers final: 24 residues processed: 123 average time/residue: 2.6871 time to fit residues: 352.9567 Evaluate side-chains 125 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9240 Z= 0.170 Angle : 0.452 6.005 12559 Z= 0.234 Chirality : 0.036 0.129 1427 Planarity : 0.003 0.038 1550 Dihedral : 9.925 73.587 1481 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.82 % Allowed : 19.96 % Favored : 77.22 % 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: 1.21 (0.26), residues: 1090 helix: 2.28 (0.26), residues: 451 sheet: -0.24 (0.51), residues: 105 loop : -0.24 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.019 0.001 PHE B 407 TYR 0.008 0.001 TYR A 403 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8469 (t0) cc_final: 0.8121 (t0) REVERT: A 326 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: B 507 TYR cc_start: 0.8650 (t80) cc_final: 0.8403 (t80) REVERT: C 113 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8039 (t) outliers start: 27 outliers final: 21 residues processed: 120 average time/residue: 2.6521 time to fit residues: 340.1225 Evaluate side-chains 121 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.0170 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9240 Z= 0.177 Angle : 0.452 5.759 12559 Z= 0.234 Chirality : 0.036 0.128 1427 Planarity : 0.004 0.044 1550 Dihedral : 9.902 73.581 1481 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.51 % Allowed : 20.59 % Favored : 76.91 % 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: 1.24 (0.26), residues: 1090 helix: 2.31 (0.25), residues: 451 sheet: -0.24 (0.51), residues: 105 loop : -0.23 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.020 0.001 PHE B 407 TYR 0.009 0.001 TYR A 403 ARG 0.006 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7446 (ttp-110) REVERT: A 323 ASP cc_start: 0.8476 (t0) cc_final: 0.8141 (t0) REVERT: A 326 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 467 ASP cc_start: 0.8333 (t0) cc_final: 0.8107 (t0) REVERT: B 507 TYR cc_start: 0.8653 (t80) cc_final: 0.8407 (t80) REVERT: C 113 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8029 (t) outliers start: 24 outliers final: 21 residues processed: 118 average time/residue: 2.6156 time to fit residues: 330.6274 Evaluate side-chains 120 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.075605 restraints weight = 49808.252| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.16 r_work: 0.2658 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9240 Z= 0.190 Angle : 0.457 6.007 12559 Z= 0.236 Chirality : 0.036 0.129 1427 Planarity : 0.003 0.038 1550 Dihedral : 9.899 73.574 1481 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 20.27 % Favored : 77.01 % 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: 1.23 (0.26), residues: 1090 helix: 2.30 (0.25), residues: 451 sheet: -0.25 (0.51), residues: 105 loop : -0.22 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.020 0.001 PHE B 407 TYR 0.009 0.001 TYR B 217 ARG 0.005 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6844.65 seconds wall clock time: 120 minutes 5.24 seconds (7205.24 seconds total)