Starting phenix.real_space_refine on Sat Jul 4 03:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_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/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ptj_17872/07_2026/8ptj_17872.cif" } 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-dev-6108/lib/python3.11/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: 2.55, per 1000 atoms: 0.14 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: 1.22 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 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: 2.42 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: 3.70 Time building geometry restraints manager: 1.67 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: 7480 17.80 - 35.60: 670 35.60 - 53.39: 250 53.39 - 71.19: 63 71.19 - 88.99: 20 Dihedral angle restraints: 8483 sinusoidal: 4776 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 8480 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: 1.450 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: 0.090 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 17.551 88.990 3550 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 are 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/Z covalent geometry : bond 0.00378 / 0.23 ( 9240) covalent geometry : angle 0.48452 / 0.27 (12559) hydrogen bonds : bond 0.13896 / 9.40 ( 398) hydrogen bonds : angle 4.94562 / 3.61 ( 1091) metal coordination : bond 0.00051 / 0.03 ( 4) metal coordination : angle 0.84953 / 0.47 ( 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 : 0.336 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: 1.0253 time to fit residues: 136.6120 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 : 0.482 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.098792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.075720 restraints weight = 47436.039| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.19 r_work: 0.2664 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9244 Z= 0.135 Angle : 0.470 4.912 12561 Z= 0.245 Chirality : 0.037 0.131 1427 Planarity : 0.004 0.041 1550 Dihedral : 9.159 73.560 1472 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.51 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 are not related in a simple way. whole: 1.16 (0.26), residues: 1090 helix: 2.18 (0.25), residues: 451 sheet: -0.28 (0.52), residues: 107 loop : -0.20 (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 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9240) covalent geometry : angle 0.47007 / 0.24 (12559) hydrogen bonds : bond 0.04525 / 3.07 ( 398) hydrogen bonds : angle 4.10211 / 3.00 ( 1091) metal coordination : bond 0.00293 / 0.15 ( 4) metal coordination : angle 0.83909 / 0.48 ( 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 130 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.537 Fit side-chains REVERT: A 34 ARG cc_start: 0.7516 (ttp-110) cc_final: 0.7192 (ttp-110) REVERT: A 323 ASP cc_start: 0.8470 (t0) cc_final: 0.8155 (t0) REVERT: A 326 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: B 497 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8304 (tp) REVERT: C 90 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8485 (mt-10) REVERT: C 93 ASP cc_start: 0.8554 (m-30) cc_final: 0.8323 (m-30) REVERT: C 113 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8110 (t) outliers start: 27 outliers final: 12 residues processed: 122 average time/residue: 1.0721 time to fit residues: 140.1685 Evaluate side-chains 112 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3116 r_free = 0.3116 target = 0.097277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.073858 restraints weight = 54884.706| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.26 r_work: 0.2630 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9244 Z= 0.170 Angle : 0.483 4.302 12561 Z= 0.252 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.037 1550 Dihedral : 8.809 73.584 1451 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.93 % Allowed : 19.44 % 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 are not related in a simple way. whole: 1.07 (0.26), residues: 1090 helix: 2.15 (0.25), residues: 450 sheet: -0.39 (0.51), residues: 107 loop : -0.28 (0.26), residues: 533 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 0.021 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/Z covalent geometry : bond 0.00392 / 0.17 ( 9240) covalent geometry : angle 0.48271 / 0.25 (12559) hydrogen bonds : bond 0.04576 / 3.09 ( 398) hydrogen bonds : angle 4.00415 / 2.92 ( 1091) metal coordination : bond 0.00707 / 0.35 ( 4) metal coordination : angle 0.66861 / 0.38 ( 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 132 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7555 (mtm180) REVERT: A 118 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: A 323 ASP cc_start: 0.8630 (t0) cc_final: 0.8217 (t0) REVERT: A 326 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: C 93 ASP cc_start: 0.8604 (m-30) cc_final: 0.8396 (m-30) REVERT: C 113 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8080 (t) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 1.0562 time to fit residues: 140.6768 Evaluate side-chains 115 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.074188 restraints weight = 46359.089| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.07 r_work: 0.2629 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9244 Z= 0.205 Angle : 0.500 4.201 12561 Z= 0.262 Chirality : 0.038 0.131 1427 Planarity : 0.004 0.039 1550 Dihedral : 8.722 73.613 1448 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.03 % Allowed : 19.85 % 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 are not related in a simple way. whole: 0.93 (0.26), residues: 1090 helix: 2.05 (0.25), residues: 450 sheet: -0.43 (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 0.023 0.001 PHE B 407 TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 ( 9240) covalent geometry : angle 0.50029 / 0.26 (12559) hydrogen bonds : bond 0.04689 / 3.17 ( 398) hydrogen bonds : angle 4.03671 / 2.95 ( 1091) metal coordination : bond 0.00972 / 0.48 ( 4) metal coordination : angle 0.55214 / 0.32 ( 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 127 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8625 (t0) cc_final: 0.8211 (t0) REVERT: A 326 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: C 93 ASP cc_start: 0.8600 (m-30) cc_final: 0.8379 (m-30) REVERT: C 113 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (t) outliers start: 29 outliers final: 18 residues processed: 117 average time/residue: 1.1223 time to fit residues: 140.5534 Evaluate side-chains 116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 339 ASP 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 89 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 388 SER 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: 3.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.097359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.074672 restraints weight = 46056.456| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.07 r_work: 0.2653 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9244 Z= 0.141 Angle : 0.469 4.033 12561 Z= 0.245 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.038 1550 Dihedral : 8.651 73.570 1448 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.93 % Allowed : 19.75 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1090 helix: 2.13 (0.25), residues: 450 sheet: -0.41 (0.46), residues: 125 loop : -0.34 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.010 0.001 TYR A 403 PHE 0.021 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/Z covalent geometry : bond 0.00326 / 0.14 ( 9240) covalent geometry : angle 0.46940 / 0.25 (12559) hydrogen bonds : bond 0.04173 / 2.82 ( 398) hydrogen bonds : angle 3.93123 / 2.88 ( 1091) metal coordination : bond 0.00401 / 0.20 ( 4) metal coordination : angle 0.76929 / 0.43 ( 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 129 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: A 323 ASP cc_start: 0.8485 (t0) cc_final: 0.8092 (t0) REVERT: A 326 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 93 ASP cc_start: 0.8608 (m-30) cc_final: 0.8386 (m-30) REVERT: C 113 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8080 (t) outliers start: 28 outliers final: 19 residues processed: 122 average time/residue: 1.1021 time to fit residues: 143.7264 Evaluate side-chains 120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 339 ASP 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 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: 0.0980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.072922 restraints weight = 54144.331| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.24 r_work: 0.2612 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9244 Z= 0.198 Angle : 0.497 4.172 12561 Z= 0.261 Chirality : 0.038 0.130 1427 Planarity : 0.004 0.040 1550 Dihedral : 8.724 73.626 1448 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 3.66 % Allowed : 19.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1090 helix: 2.04 (0.25), residues: 450 sheet: -0.48 (0.46), residues: 125 loop : -0.37 (0.27), 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 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 9240) covalent geometry : angle 0.49736 / 0.26 (12559) hydrogen bonds : bond 0.04565 / 3.09 ( 398) hydrogen bonds : angle 4.00827 / 2.93 ( 1091) metal coordination : bond 0.00899 / 0.45 ( 4) metal coordination : angle 0.60696 / 0.35 ( 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 : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8618 (t0) cc_final: 0.8194 (t0) REVERT: A 326 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: C 93 ASP cc_start: 0.8638 (m-30) cc_final: 0.8424 (m-30) REVERT: C 113 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8103 (t) outliers start: 35 outliers final: 20 residues processed: 122 average time/residue: 1.2654 time to fit residues: 164.2878 Evaluate side-chains 119 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.073472 restraints weight = 56283.258| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.29 r_work: 0.2614 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9244 Z= 0.157 Angle : 0.478 4.435 12561 Z= 0.250 Chirality : 0.037 0.130 1427 Planarity : 0.004 0.039 1550 Dihedral : 8.699 73.593 1448 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.03 % Allowed : 19.85 % 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 are not related in a simple way. whole: 0.98 (0.26), residues: 1090 helix: 2.11 (0.25), residues: 450 sheet: -0.47 (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 0.021 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/Z covalent geometry : bond 0.00362 / 0.16 ( 9240) covalent geometry : angle 0.47782 / 0.25 (12559) hydrogen bonds : bond 0.04253 / 2.87 ( 398) hydrogen bonds : angle 3.95587 / 2.89 ( 1091) metal coordination : bond 0.00489 / 0.24 ( 4) metal coordination : angle 0.65061 / 0.37 ( 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: 29 poor density : 100 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8559 (t0) cc_final: 0.8137 (t0) REVERT: A 326 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: C 93 ASP cc_start: 0.8634 (m-30) cc_final: 0.8420 (m-30) REVERT: C 113 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8102 (t) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 1.1693 time to fit residues: 154.4026 Evaluate side-chains 120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS 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 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 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: 1.9990 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.074978 restraints weight = 60468.798| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.37 r_work: 0.2626 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1289 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= 0.105 Angle : 0.452 4.627 12561 Z= 0.235 Chirality : 0.036 0.130 1427 Planarity : 0.003 0.038 1550 Dihedral : 8.604 73.560 1448 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.51 % Allowed : 20.79 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1090 helix: 2.25 (0.25), residues: 451 sheet: -0.40 (0.46), residues: 125 loop : -0.28 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.009 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/Z covalent geometry : bond 0.00241 / 0.11 ( 9240) covalent geometry : angle 0.45234 / 0.24 (12559) hydrogen bonds : bond 0.03689 / 2.50 ( 398) hydrogen bonds : angle 3.79710 / 2.78 ( 1091) metal coordination : bond 0.00082 / 0.04 ( 4) metal coordination : angle 0.65150 / 0.36 ( 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: 24 poor density : 101 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8401 (t0) cc_final: 0.8039 (t0) REVERT: A 326 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: B 57 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: C 93 ASP cc_start: 0.8645 (m-30) cc_final: 0.8412 (m-30) REVERT: C 113 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8067 (t) outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 1.0517 time to fit residues: 135.8245 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS 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 326 GLU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 112 ILE 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 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 Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3125 r_free = 0.3125 target = 0.097924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.074477 restraints weight = 59505.501| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.35 r_work: 0.2604 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1337 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= 0.128 Angle : 0.458 4.494 12561 Z= 0.238 Chirality : 0.036 0.128 1427 Planarity : 0.004 0.039 1550 Dihedral : 8.544 73.593 1445 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 2.61 % Allowed : 20.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1090 helix: 2.23 (0.25), residues: 451 sheet: -0.42 (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 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9240) covalent geometry : angle 0.45780 / 0.24 (12559) hydrogen bonds : bond 0.03869 / 2.62 ( 398) hydrogen bonds : angle 3.81263 / 2.79 ( 1091) metal coordination : bond 0.00227 / 0.11 ( 4) metal coordination : angle 0.64564 / 0.36 ( 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 123 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8586 (t0) cc_final: 0.8206 (t0) REVERT: A 326 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: B 57 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: C 93 ASP cc_start: 0.8638 (m-30) cc_final: 0.8422 (m-30) REVERT: C 113 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8087 (t) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 1.1231 time to fit residues: 142.2978 Evaluate side-chains 119 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS 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 326 GLU Chi-restraints excluded: chain B residue 57 GLN 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 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 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 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 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.074825 restraints weight = 53054.023| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.32 r_work: 0.2609 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9244 Z= 0.118 Angle : 0.457 6.258 12561 Z= 0.237 Chirality : 0.036 0.128 1427 Planarity : 0.004 0.039 1550 Dihedral : 8.540 73.574 1445 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.19 % Allowed : 21.11 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1090 helix: 2.26 (0.25), residues: 451 sheet: -0.40 (0.46), residues: 125 loop : -0.28 (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 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9240) covalent geometry : angle 0.45722 / 0.24 (12559) hydrogen bonds : bond 0.03785 / 2.56 ( 398) hydrogen bonds : angle 3.78500 / 2.77 ( 1091) metal coordination : bond 0.00121 / 0.06 ( 4) metal coordination : angle 0.62433 / 0.35 ( 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 122 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8501 (t0) cc_final: 0.8125 (t0) REVERT: A 326 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: B 57 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: C 90 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8394 (mt-10) REVERT: C 93 ASP cc_start: 0.8634 (m-30) cc_final: 0.8407 (m-30) REVERT: C 113 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8084 (t) outliers start: 21 outliers final: 17 residues processed: 118 average time/residue: 1.2041 time to fit residues: 152.1038 Evaluate side-chains 120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 44 CYS 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 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 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 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 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3114 r_free = 0.3114 target = 0.097200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.073932 restraints weight = 51450.144| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.29 r_work: 0.2615 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9244 Z= 0.155 Angle : 0.475 5.826 12561 Z= 0.247 Chirality : 0.037 0.129 1427 Planarity : 0.004 0.039 1550 Dihedral : 8.589 73.591 1445 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.51 % Allowed : 20.79 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1090 helix: 2.22 (0.25), residues: 450 sheet: -0.45 (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/Z covalent geometry : bond 0.00360 / 0.16 ( 9240) covalent geometry : angle 0.47500 / 0.25 (12559) hydrogen bonds : bond 0.04098 / 2.77 ( 398) hydrogen bonds : angle 3.85452 / 2.82 ( 1091) metal coordination : bond 0.00506 / 0.25 ( 4) metal coordination : angle 0.58357 / 0.33 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5477.09 seconds wall clock time: 93 minutes 19.40 seconds (5599.40 seconds total)