Starting phenix.real_space_refine on Sun Aug 24 07:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_17872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_17872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_17872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_17872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2025/8ptj_17872.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.63, per 1000 atoms: 0.15 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 - 3.00 Amino acid : True - 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: 1.44 Conformation dependent library (CDL) restraints added in 767.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.41 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: 3.68 Time building geometry restraints manager: 2.00 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: 0.00 - 1.54: 32182 1.54 - 3.08: 409 3.08 - 4.62: 53 4.62 - 6.17: 6 6.17 - 7.71: 1 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 2.450 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU B 381 " pdb=" H PHE B 420 " model vdw 1.620 2.450 nonbonded pdb=" O PHE A 55 " pdb="HH11 ARG A 62 " model vdw 1.642 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- 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 9244 Z= 0.232 Angle : 0.485 7.708 12561 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG A 34 TYR 0.008 0.001 TYR A 403 PHE 0.018 0.001 PHE B 407 TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9240) covalent geometry : angle 0.48452 (12559) hydrogen bonds : bond 0.13896 ( 398) hydrogen bonds : angle 4.94562 ( 1091) metal coordination : bond 0.00051 ( 4) metal coordination : angle 0.84953 ( 2) *********************** 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 to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.501 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: 1.1796 time to fit residues: 156.3673 Evaluate side-chains 118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.098798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.075728 restraints weight = 47840.422| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.19 r_work: 0.2666 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 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 = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9244 Z= 0.133 Angle : 0.471 4.850 12561 Z= 0.245 Chirality : 0.037 0.134 1427 Planarity : 0.004 0.041 1550 Dihedral : 10.600 73.552 1508 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.82 % Allowed : 19.54 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.26), residues: 1090 helix: 2.17 (0.25), residues: 451 sheet: -0.29 (0.52), residues: 107 loop : -0.21 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.010 0.001 TYR A 403 PHE 0.019 0.001 PHE B 407 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9240) covalent geometry : angle 0.47093 (12559) hydrogen bonds : bond 0.04527 ( 398) hydrogen bonds : angle 4.11266 ( 1091) metal coordination : bond 0.00304 ( 4) metal coordination : angle 0.83174 ( 2) *********************** 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 129 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.310 Fit side-chains REVERT: A 34 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7185 (ttp-110) REVERT: A 323 ASP cc_start: 0.8468 (t0) cc_final: 0.8154 (t0) REVERT: A 326 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: B 497 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8324 (tp) REVERT: C 93 ASP cc_start: 0.8555 (m-30) cc_final: 0.8322 (m-30) REVERT: C 113 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8113 (t) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 1.3387 time to fit residues: 172.0222 Evaluate side-chains 113 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 213 ASP 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 B residue 497 LEU Chi-restraints excluded: chain C residue 113 VAL 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 91 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.098541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.075239 restraints weight = 53137.098| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.23 r_work: 0.2660 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9244 Z= 0.133 Angle : 0.459 4.325 12561 Z= 0.239 Chirality : 0.036 0.127 1427 Planarity : 0.003 0.036 1550 Dihedral : 10.259 73.558 1487 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.72 % Allowed : 19.85 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1090 helix: 2.21 (0.25), residues: 451 sheet: -0.31 (0.52), residues: 107 loop : -0.26 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.011 0.001 TYR A 403 PHE 0.020 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9240) covalent geometry : angle 0.45939 (12559) hydrogen bonds : bond 0.04207 ( 398) hydrogen bonds : angle 3.93666 ( 1091) metal coordination : bond 0.00332 ( 4) metal coordination : angle 0.69214 ( 2) *********************** 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 131 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8489 (t0) cc_final: 0.8116 (t0) REVERT: A 326 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: B 57 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: C 93 ASP cc_start: 0.8594 (m-30) cc_final: 0.8306 (m-30) REVERT: C 113 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8126 (t) outliers start: 26 outliers final: 12 residues processed: 124 average time/residue: 1.4102 time to fit residues: 186.6734 Evaluate side-chains 114 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU 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 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 83 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.074239 restraints weight = 45793.229| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.06 r_work: 0.2643 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9244 Z= 0.188 Angle : 0.492 5.462 12561 Z= 0.257 Chirality : 0.038 0.130 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.103 73.597 1482 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.82 % Allowed : 19.44 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1090 helix: 2.12 (0.25), residues: 450 sheet: -0.36 (0.47), residues: 125 loop : -0.35 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.011 0.001 TYR A 403 PHE 0.021 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9240) covalent geometry : angle 0.49161 (12559) hydrogen bonds : bond 0.04516 ( 398) hydrogen bonds : angle 3.98051 ( 1091) metal coordination : bond 0.00855 ( 4) metal coordination : angle 0.61498 ( 2) *********************** 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 128 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: A 323 ASP cc_start: 0.8603 (t0) cc_final: 0.8204 (t0) REVERT: A 326 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: C 93 ASP cc_start: 0.8605 (m-30) cc_final: 0.8396 (m-30) REVERT: C 113 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8096 (t) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 1.3939 time to fit residues: 175.9448 Evaluate side-chains 117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP 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 326 GLU 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 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 83 ARG Chi-restraints excluded: chain C residue 113 VAL 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 7 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.073957 restraints weight = 45894.207| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.06 r_work: 0.2640 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9244 Z= 0.185 Angle : 0.487 4.888 12561 Z= 0.255 Chirality : 0.038 0.129 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.105 73.603 1482 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.13 % Allowed : 19.44 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1090 helix: 2.08 (0.25), residues: 450 sheet: -0.41 (0.46), residues: 125 loop : -0.36 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.011 0.001 TYR A 403 PHE 0.022 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9240) covalent geometry : angle 0.48696 (12559) hydrogen bonds : bond 0.04486 ( 398) hydrogen bonds : angle 3.98620 ( 1091) metal coordination : bond 0.00764 ( 4) metal coordination : angle 0.63606 ( 2) *********************** 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 130 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7477 (mtm180) REVERT: A 118 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: A 323 ASP cc_start: 0.8561 (t0) cc_final: 0.8147 (t0) REVERT: A 326 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: C 90 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8375 (mt-10) REVERT: C 93 ASP cc_start: 0.8609 (m-30) cc_final: 0.8401 (m-30) REVERT: C 113 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8091 (t) outliers start: 30 outliers final: 18 residues processed: 120 average time/residue: 1.3280 time to fit residues: 170.2071 Evaluate side-chains 121 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP 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 326 GLU 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 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 449 SER 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 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.096072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.072762 restraints weight = 53871.819| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.24 r_work: 0.2609 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9244 Z= 0.206 Angle : 0.502 4.891 12561 Z= 0.263 Chirality : 0.038 0.131 1427 Planarity : 0.004 0.040 1550 Dihedral : 10.153 73.606 1482 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 3.66 % Allowed : 19.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.26), residues: 1090 helix: 2.02 (0.25), residues: 450 sheet: -0.48 (0.46), residues: 125 loop : -0.40 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.011 0.001 TYR A 403 PHE 0.022 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9240) covalent geometry : angle 0.50220 (12559) hydrogen bonds : bond 0.04619 ( 398) hydrogen bonds : angle 4.02779 ( 1091) metal coordination : bond 0.00923 ( 4) metal coordination : angle 0.58526 ( 2) *********************** 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 to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7444 (mtm180) REVERT: A 323 ASP cc_start: 0.8630 (t0) cc_final: 0.8201 (t0) REVERT: A 326 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 93 ASP cc_start: 0.8622 (m-30) cc_final: 0.8400 (m-30) REVERT: C 113 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8100 (t) outliers start: 35 outliers final: 22 residues processed: 121 average time/residue: 1.4972 time to fit residues: 191.6333 Evaluate side-chains 123 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU 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 252 LEU Chi-restraints excluded: chain B residue 381 GLU 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 449 SER 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 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.071925 restraints weight = 57061.505| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.29 r_work: 0.2594 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9244 Z= 0.236 Angle : 0.521 4.393 12561 Z= 0.274 Chirality : 0.039 0.132 1427 Planarity : 0.004 0.041 1550 Dihedral : 10.236 73.634 1482 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 3.24 % Allowed : 20.27 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.25), residues: 1090 helix: 1.96 (0.25), residues: 450 sheet: -0.55 (0.48), residues: 113 loop : -0.45 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.011 0.001 TYR A 403 PHE 0.024 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 9240) covalent geometry : angle 0.52093 (12559) hydrogen bonds : bond 0.04838 ( 398) hydrogen bonds : angle 4.10183 ( 1091) metal coordination : bond 0.01124 ( 4) metal coordination : angle 0.50043 ( 2) *********************** 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 129 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: A 323 ASP cc_start: 0.8692 (t0) cc_final: 0.8241 (t0) REVERT: A 326 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: C 93 ASP cc_start: 0.8639 (m-30) cc_final: 0.8419 (m-30) REVERT: C 113 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8133 (t) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 1.2639 time to fit residues: 162.4200 Evaluate side-chains 121 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 391 GLU 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 381 GLU 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 449 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.097684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.074150 restraints weight = 61288.184| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.39 r_work: 0.2630 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9244 Z= 0.109 Angle : 0.463 4.735 12561 Z= 0.241 Chirality : 0.036 0.131 1427 Planarity : 0.004 0.039 1550 Dihedral : 10.114 73.582 1482 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1090 helix: 2.16 (0.25), residues: 450 sheet: -0.41 (0.46), residues: 125 loop : -0.35 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.010 0.001 TYR A 403 PHE 0.020 0.001 PHE B 407 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9240) covalent geometry : angle 0.46277 (12559) hydrogen bonds : bond 0.03928 ( 398) hydrogen bonds : angle 3.91560 ( 1091) metal coordination : bond 0.00060 ( 4) metal coordination : angle 0.70888 ( 2) *********************** 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 125 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8476 (t0) cc_final: 0.8076 (t0) REVERT: A 326 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: C 93 ASP cc_start: 0.8638 (m-30) cc_final: 0.8413 (m-30) REVERT: C 113 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8088 (t) outliers start: 25 outliers final: 17 residues processed: 119 average time/residue: 1.3729 time to fit residues: 174.5592 Evaluate side-chains 117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 255 MET 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 252 LEU Chi-restraints excluded: chain B residue 381 GLU 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 449 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 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 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 0.0060 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN C 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.075566 restraints weight = 57918.909| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.33 r_work: 0.2670 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9244 Z= 0.094 Angle : 0.450 6.081 12561 Z= 0.233 Chirality : 0.036 0.128 1427 Planarity : 0.003 0.039 1550 Dihedral : 9.946 73.567 1481 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.30 % Allowed : 20.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1090 helix: 2.29 (0.25), residues: 451 sheet: -0.34 (0.47), residues: 125 loop : -0.28 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 34 TYR 0.010 0.001 TYR B 217 PHE 0.018 0.001 PHE B 407 TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9240) covalent geometry : angle 0.44960 (12559) hydrogen bonds : bond 0.03510 ( 398) hydrogen bonds : angle 3.75336 ( 1091) metal coordination : bond 0.00135 ( 4) metal coordination : angle 0.79549 ( 2) *********************** 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 125 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8283 (t0) cc_final: 0.7931 (t0) REVERT: A 326 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 57 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: C 93 ASP cc_start: 0.8627 (m-30) cc_final: 0.8398 (m-30) REVERT: C 113 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8068 (t) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 1.4778 time to fit residues: 188.4128 Evaluate side-chains 114 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 236 THR 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 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 462 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 113 VAL 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 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.097441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.074243 restraints weight = 52332.795| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.28 r_work: 0.2633 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9244 Z= 0.144 Angle : 0.469 5.798 12561 Z= 0.244 Chirality : 0.037 0.128 1427 Planarity : 0.004 0.040 1550 Dihedral : 9.976 73.589 1481 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.99 % Allowed : 21.63 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1090 helix: 2.26 (0.25), residues: 450 sheet: -0.38 (0.46), residues: 125 loop : -0.30 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.010 0.001 TYR A 403 PHE 0.020 0.001 PHE B 407 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9240) covalent geometry : angle 0.46931 (12559) hydrogen bonds : bond 0.04010 ( 398) hydrogen bonds : angle 3.85164 ( 1091) metal coordination : bond 0.00431 ( 4) metal coordination : angle 0.79295 ( 2) ********************** 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 118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8625 (t0) cc_final: 0.8248 (t0) REVERT: A 326 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: C 93 ASP cc_start: 0.8624 (m-30) cc_final: 0.8408 (m-30) REVERT: C 113 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8113 (t) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 1.5772 time to fit residues: 192.7138 Evaluate side-chains 115 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 326 GLU 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 419 SER Chi-restraints excluded: chain B residue 444 ASP 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 388 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 C 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.075089 restraints weight = 50660.922| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.27 r_work: 0.2635 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9244 Z= 0.118 Angle : 0.459 5.962 12561 Z= 0.238 Chirality : 0.036 0.129 1427 Planarity : 0.004 0.039 1550 Dihedral : 9.965 73.576 1481 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.09 % Allowed : 21.63 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.26), residues: 1090 helix: 2.28 (0.25), residues: 451 sheet: -0.38 (0.46), residues: 125 loop : -0.29 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.010 0.001 TYR A 403 PHE 0.019 0.001 PHE B 407 TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9240) covalent geometry : angle 0.45846 (12559) hydrogen bonds : bond 0.03784 ( 398) hydrogen bonds : angle 3.80779 ( 1091) metal coordination : bond 0.00112 ( 4) metal coordination : angle 0.78069 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.55 seconds wall clock time: 108 minutes 38.04 seconds (6518.04 seconds total)