Starting phenix.real_space_refine on Fri Sep 11 13:54:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbv_21599/09_2026/6wbv_21599.map" } resolution = 2.5 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= -0.013 sd= 0.959 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3344 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 2 5.49 5 S 47 5.16 5 C 4398 2.51 5 N 1114 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3262 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1703 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' CO': 2, 'AGA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2181 SG CYS A 326 78.631 63.845 45.666 1.00 49.12 S Time building chain proxies: 1.97, per 1000 atoms: 0.29 Number of scatterers: 6860 At special positions: 0 Unit cell: (113.424, 110.088, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 47 16.00 P 2 15.00 O 1297 8.00 N 1114 7.00 C 4398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 13 " distance=2.02 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS H 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 548.1 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 47.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.503A pdb=" N ALA A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 125 through 156 removed outlier: 4.247A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 166 through 199 removed outlier: 3.811A pdb=" N LEU A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.975A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 368 through 391 removed outlier: 3.540A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 484 removed outlier: 4.491A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.591A pdb=" N ILE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 546 removed outlier: 3.573A pdb=" N GLY A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 187 through 191 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 205 through 208 Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.014A pdb=" N MET L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR L 53 " --> pdb=" O MET L 37 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.141A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.815A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.240A pdb=" N TRP L 152 " --> pdb=" O ARG L 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.616A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.551A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.987A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.261A pdb=" N THR H 142 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL H 188 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY H 144 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 186 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.261A pdb=" N THR H 142 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL H 188 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY H 144 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 186 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159 470 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1060 1.26 - 1.40: 1747 1.40 - 1.55: 4118 1.55 - 1.69: 12 1.69 - 1.83: 68 Bond restraints: 7005 Sorted by residual: bond pdb=" C SER L 32 " pdb=" O SER L 32 " ideal model delta sigma weight residual 1.243 1.122 0.121 9.50e-03 1.11e+04 1.63e+02 bond pdb=" C TYR L 34 " pdb=" O TYR L 34 " ideal model delta sigma weight residual 1.234 1.114 0.120 1.28e-02 6.10e+03 8.84e+01 bond pdb=" CA ALA L 31 " pdb=" C ALA L 31 " ideal model delta sigma weight residual 1.520 1.427 0.093 1.16e-02 7.43e+03 6.44e+01 bond pdb=" CA TYR L 34 " pdb=" C TYR L 34 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.21e-02 6.83e+03 6.10e+01 bond pdb=" C ALA L 31 " pdb=" O ALA L 31 " ideal model delta sigma weight residual 1.235 1.175 0.059 1.13e-02 7.83e+03 2.77e+01 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 9427 3.30 - 6.60: 101 6.60 - 9.90: 14 9.90 - 13.20: 3 13.20 - 16.49: 2 Bond angle restraints: 9547 Sorted by residual: angle pdb=" C ASN A 516 " pdb=" N PRO A 517 " pdb=" CA PRO A 517 " ideal model delta sigma weight residual 119.28 127.37 -8.09 1.10e+00 8.26e-01 5.41e+01 angle pdb=" C ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta sigma weight residual 110.04 100.16 9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" O5 AGA A 701 " pdb=" P1 AGA A 701 " pdb=" O6 AGA A 701 " ideal model delta sigma weight residual 93.68 110.17 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O5 AGA A 702 " pdb=" P1 AGA A 702 " pdb=" O6 AGA A 702 " ideal model delta sigma weight residual 93.68 109.83 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N PRO A 515 " pdb=" CA PRO A 515 " pdb=" C PRO A 515 " ideal model delta sigma weight residual 112.47 121.47 -9.00 2.06e+00 2.36e-01 1.91e+01 ... (remaining 9542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3717 17.21 - 34.42: 274 34.42 - 51.63: 85 51.63 - 68.84: 27 68.84 - 86.05: 13 Dihedral angle restraints: 4116 sinusoidal: 1539 harmonic: 2577 Sorted by residual: dihedral pdb=" C SER L 32 " pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C ALA L 55 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta harmonic sigma weight residual -122.60 -110.94 -11.66 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1086 0.111 - 0.221: 33 0.221 - 0.331: 2 0.331 - 0.442: 2 0.442 - 0.552: 1 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA SER L 32 " pdb=" N SER L 32 " pdb=" C SER L 32 " pdb=" CB SER L 32 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TRP H 103 " pdb=" N TRP H 103 " pdb=" C TRP H 103 " pdb=" CB TRP H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PRO A 515 " pdb=" N PRO A 515 " pdb=" C PRO A 515 " pdb=" CB PRO A 515 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 1121 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 516 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ASN A 516 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN A 516 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 517 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C SER L 71 " 0.047 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY L 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 35 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN H 35 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN H 35 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP H 36 " 0.016 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 25 2.42 - 3.04: 4166 3.04 - 3.66: 10377 3.66 - 4.28: 16019 4.28 - 4.90: 26508 Nonbonded interactions: 57095 Sorted by model distance: nonbonded pdb="CO CO A 704 " pdb=" O HOH A 806 " model vdw 1.797 2.220 nonbonded pdb=" O THR B 25 " pdb="CO CO A 704 " model vdw 1.798 2.220 nonbonded pdb=" ND2 ASN L 95 " pdb=" O TRP H 103 " model vdw 1.887 3.120 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 704 " model vdw 2.111 2.300 nonbonded pdb=" OG SER A 35 " pdb=" OE1 GLU A 219 " model vdw 2.113 3.040 ... (remaining 57090 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.050 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.006 0.121 7014 Z= 0.389 Angle : 0.936 16.494 9565 Z= 0.502 Chirality : 0.054 0.552 1124 Planarity : 0.007 0.067 1176 Dihedral : 15.295 86.050 2439 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.26 % Allowed : 9.05 % Favored : 86.68 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 18.42 % 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: -0.54 (0.26), residues: 879 helix: -0.19 (0.22), residues: 382 sheet: 0.01 (0.33), residues: 226 loop : -0.63 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 97 TYR 0.024 0.002 TYR H 78 PHE 0.023 0.002 PHE L 75 TRP 0.041 0.003 TRP L 167 HIS 0.005 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.39 ( 7005) covalent geometry : angle 0.93528 / 0.50 ( 9547) SS BOND : bond 0.00872 / 0.55 ( 9) SS BOND : angle 1.24634 / 0.76 ( 18) hydrogen bonds : bond 0.12386 / 8.07 ( 450) hydrogen bonds : angle 6.04241 / 4.39 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 341 ILE cc_start: 0.8536 (mp) cc_final: 0.8291 (mm) REVERT: A 364 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7895 (ttp-110) REVERT: A 366 LYS cc_start: 0.8414 (tppt) cc_final: 0.8202 (mptp) REVERT: A 516 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (m-40) REVERT: L 49 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (tptp) REVERT: H 16 GLN cc_start: 0.8131 (mt0) cc_final: 0.7927 (mt0) REVERT: H 216 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6492 (pm20) outliers start: 32 outliers final: 11 residues processed: 157 average time/residue: 0.4825 time to fit residues: 80.4172 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 HIS A 86 ASN A 99 GLN A 141 ASN A 155 GLN A 174 ASN A 185 ASN A 481 GLN A 496 GLN L 142 ASN L 149 ASN L 194 ASN L 216 ASN H 3 GLN H 77 HIS H 83 ASN H 98 GLN H 196 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112673 restraints weight = 15363.691| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.31 r_work: 0.3380 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7014 Z= 0.138 Angle : 0.584 8.319 9565 Z= 0.307 Chirality : 0.042 0.154 1124 Planarity : 0.005 0.051 1176 Dihedral : 9.613 90.341 1010 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.06 % Allowed : 13.45 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.34 (0.28), residues: 879 helix: 1.83 (0.25), residues: 393 sheet: 0.69 (0.35), residues: 222 loop : -0.28 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 96 TYR 0.024 0.002 TYR H 78 PHE 0.014 0.002 PHE L 213 TRP 0.017 0.002 TRP H 34 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7005) covalent geometry : angle 0.58334 / 0.31 ( 9547) SS BOND : bond 0.00604 / 0.39 ( 9) SS BOND : angle 0.86966 / 0.53 ( 18) hydrogen bonds : bond 0.05701 / 3.81 ( 450) hydrogen bonds : angle 4.43884 / 3.22 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8448 (mttt) REVERT: A 317 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 341 ILE cc_start: 0.8552 (mp) cc_final: 0.8278 (mm) REVERT: A 378 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8303 (mp) REVERT: L 49 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8764 (mttt) REVERT: H 16 GLN cc_start: 0.8374 (mt0) cc_final: 0.8061 (mt0) REVERT: H 81 GLN cc_start: 0.8285 (tt0) cc_final: 0.8067 (tt0) REVERT: H 183 SER cc_start: 0.9023 (p) cc_final: 0.8807 (p) outliers start: 23 outliers final: 11 residues processed: 120 average time/residue: 0.5370 time to fit residues: 68.0475 Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 76 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112291 restraints weight = 12299.938| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3367 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7014 Z= 0.154 Angle : 0.590 9.265 9565 Z= 0.307 Chirality : 0.042 0.174 1124 Planarity : 0.005 0.052 1176 Dihedral : 8.942 83.244 996 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 14.78 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.83 (0.28), residues: 879 helix: 2.27 (0.26), residues: 393 sheet: 1.08 (0.35), residues: 213 loop : -0.23 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.025 0.002 TYR H 78 PHE 0.012 0.002 PHE A 295 TRP 0.020 0.002 TRP H 34 HIS 0.005 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7005) covalent geometry : angle 0.58924 / 0.31 ( 9547) SS BOND : bond 0.00654 / 0.44 ( 9) SS BOND : angle 1.01584 / 0.62 ( 18) hydrogen bonds : bond 0.05952 / 3.99 ( 450) hydrogen bonds : angle 4.35370 / 3.15 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8433 (mttt) REVERT: A 317 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 341 ILE cc_start: 0.8593 (mp) cc_final: 0.8264 (mm) REVERT: A 364 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7733 (ttp-110) REVERT: A 378 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8383 (mp) REVERT: L 49 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8373 (tptp) REVERT: H 16 GLN cc_start: 0.8379 (mt0) cc_final: 0.8045 (mt0) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 0.5151 time to fit residues: 65.7884 Evaluate side-chains 113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114740 restraints weight = 11108.357| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.97 r_work: 0.3405 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7014 Z= 0.121 Angle : 0.543 9.908 9565 Z= 0.280 Chirality : 0.040 0.168 1124 Planarity : 0.005 0.050 1176 Dihedral : 8.632 78.948 992 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.73 % Allowed : 14.65 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.15 (0.28), residues: 879 helix: 2.59 (0.26), residues: 393 sheet: 1.16 (0.35), residues: 210 loop : -0.07 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 112 TYR 0.022 0.001 TYR H 78 PHE 0.011 0.001 PHE L 213 TRP 0.015 0.001 TRP H 34 HIS 0.004 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7005) covalent geometry : angle 0.53956 / 0.28 ( 9547) SS BOND : bond 0.00543 / 0.35 ( 9) SS BOND : angle 1.55359 / 0.75 ( 18) hydrogen bonds : bond 0.05127 / 3.43 ( 450) hydrogen bonds : angle 4.14781 / 3.00 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8429 (mttt) REVERT: A 317 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 341 ILE cc_start: 0.8565 (mp) cc_final: 0.8280 (mm) REVERT: L 18 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7415 (ptm160) REVERT: L 49 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8340 (tptm) REVERT: H 16 GLN cc_start: 0.8344 (mt0) cc_final: 0.8029 (mt0) outliers start: 28 outliers final: 15 residues processed: 122 average time/residue: 0.5232 time to fit residues: 67.3208 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113100 restraints weight = 11108.767| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.96 r_work: 0.3379 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7014 Z= 0.144 Angle : 0.567 10.276 9565 Z= 0.293 Chirality : 0.041 0.184 1124 Planarity : 0.005 0.050 1176 Dihedral : 8.466 76.334 988 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.60 % Allowed : 15.05 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.19 (0.29), residues: 879 helix: 2.58 (0.26), residues: 393 sheet: 1.27 (0.35), residues: 210 loop : -0.04 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 112 TYR 0.024 0.002 TYR H 78 PHE 0.012 0.002 PHE A 295 TRP 0.018 0.001 TRP H 34 HIS 0.005 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7005) covalent geometry : angle 0.56281 / 0.29 ( 9547) SS BOND : bond 0.00633 / 0.41 ( 9) SS BOND : angle 1.69262 / 0.82 ( 18) hydrogen bonds : bond 0.05598 / 3.76 ( 450) hydrogen bonds : angle 4.20073 / 3.03 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8420 (mttt) REVERT: A 317 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 341 ILE cc_start: 0.8569 (mp) cc_final: 0.8277 (mm) REVERT: L 18 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7413 (ptm160) REVERT: L 49 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8364 (tptm) REVERT: H 16 GLN cc_start: 0.8353 (mt0) cc_final: 0.8009 (mt0) outliers start: 27 outliers final: 18 residues processed: 118 average time/residue: 0.5050 time to fit residues: 63.0562 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 84 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.165734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115986 restraints weight = 20338.064| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.95 r_work: 0.3376 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7014 Z= 0.105 Angle : 0.511 10.338 9565 Z= 0.261 Chirality : 0.039 0.155 1124 Planarity : 0.004 0.047 1176 Dihedral : 8.204 71.100 988 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 16.11 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.49 (0.29), residues: 879 helix: 2.86 (0.26), residues: 393 sheet: 1.41 (0.35), residues: 212 loop : 0.05 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 112 TYR 0.020 0.001 TYR H 78 PHE 0.011 0.001 PHE A 295 TRP 0.013 0.001 TRP H 34 HIS 0.006 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7005) covalent geometry : angle 0.50943 / 0.26 ( 9547) SS BOND : bond 0.00426 / 0.27 ( 9) SS BOND : angle 1.09313 / 0.56 ( 18) hydrogen bonds : bond 0.04555 / 3.05 ( 450) hydrogen bonds : angle 3.97847 / 2.87 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8402 (mttt) REVERT: A 341 ILE cc_start: 0.8510 (mp) cc_final: 0.8235 (mm) REVERT: L 49 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8351 (tptm) REVERT: L 182 THR cc_start: 0.8074 (m) cc_final: 0.7582 (t) REVERT: H 16 GLN cc_start: 0.8334 (mt0) cc_final: 0.8019 (mt0) outliers start: 21 outliers final: 12 residues processed: 114 average time/residue: 0.5731 time to fit residues: 68.9245 Evaluate side-chains 108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111283 restraints weight = 12418.682| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.06 r_work: 0.3383 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7014 Z= 0.134 Angle : 0.552 10.401 9565 Z= 0.284 Chirality : 0.041 0.182 1124 Planarity : 0.005 0.047 1176 Dihedral : 7.732 69.919 984 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.33 % Allowed : 15.98 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.42 (0.29), residues: 879 helix: 2.72 (0.26), residues: 393 sheet: 1.51 (0.35), residues: 210 loop : 0.03 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 112 TYR 0.023 0.001 TYR H 78 PHE 0.012 0.001 PHE A 295 TRP 0.017 0.001 TRP H 34 HIS 0.006 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7005) covalent geometry : angle 0.54879 / 0.28 ( 9547) SS BOND : bond 0.00599 / 0.38 ( 9) SS BOND : angle 1.45958 / 0.74 ( 18) hydrogen bonds : bond 0.05317 / 3.57 ( 450) hydrogen bonds : angle 4.09062 / 2.96 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8414 (mttt) REVERT: A 341 ILE cc_start: 0.8535 (mp) cc_final: 0.8265 (mm) REVERT: L 18 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7433 (ptm160) REVERT: L 49 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8359 (tptm) REVERT: H 16 GLN cc_start: 0.8302 (mt0) cc_final: 0.7963 (mt0) outliers start: 25 outliers final: 19 residues processed: 117 average time/residue: 0.5222 time to fit residues: 64.7238 Evaluate side-chains 121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5360 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.161196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111086 restraints weight = 10828.803| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.94 r_work: 0.3382 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7014 Z= 0.146 Angle : 0.563 10.456 9565 Z= 0.291 Chirality : 0.041 0.183 1124 Planarity : 0.005 0.047 1176 Dihedral : 7.758 69.844 984 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.06 % Allowed : 16.11 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.36 (0.29), residues: 879 helix: 2.62 (0.25), residues: 393 sheet: 1.54 (0.36), residues: 212 loop : 0.01 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 112 TYR 0.025 0.002 TYR H 78 PHE 0.012 0.002 PHE A 295 TRP 0.019 0.002 TRP H 34 HIS 0.008 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7005) covalent geometry : angle 0.56055 / 0.29 ( 9547) SS BOND : bond 0.00637 / 0.40 ( 9) SS BOND : angle 1.35483 / 0.73 ( 18) hydrogen bonds : bond 0.05603 / 3.76 ( 450) hydrogen bonds : angle 4.15974 / 3.00 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8442 (mttt) REVERT: A 341 ILE cc_start: 0.8559 (mp) cc_final: 0.8297 (mm) REVERT: L 18 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7519 (ptm160) REVERT: L 49 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8369 (tptm) REVERT: L 182 THR cc_start: 0.8127 (m) cc_final: 0.7655 (t) REVERT: H 16 GLN cc_start: 0.8292 (mt0) cc_final: 0.7945 (mt0) outliers start: 23 outliers final: 20 residues processed: 111 average time/residue: 0.5505 time to fit residues: 64.5229 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.163470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113917 restraints weight = 10855.851| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.93 r_work: 0.3418 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7014 Z= 0.112 Angle : 0.520 10.472 9565 Z= 0.267 Chirality : 0.040 0.159 1124 Planarity : 0.005 0.046 1176 Dihedral : 7.469 66.327 984 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.40 % Allowed : 17.31 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.56 (0.29), residues: 879 helix: 2.84 (0.26), residues: 393 sheet: 1.62 (0.36), residues: 212 loop : 0.03 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.021 0.001 TYR H 78 PHE 0.011 0.001 PHE A 295 TRP 0.016 0.001 TRP H 34 HIS 0.007 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7005) covalent geometry : angle 0.51805 / 0.27 ( 9547) SS BOND : bond 0.00481 / 0.30 ( 9) SS BOND : angle 1.05807 / 0.57 ( 18) hydrogen bonds : bond 0.04769 / 3.20 ( 450) hydrogen bonds : angle 3.99796 / 2.89 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8384 (tttt) REVERT: A 85 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8863 (mmtp) REVERT: A 296 ARG cc_start: 0.8403 (mtm180) cc_final: 0.8071 (mtt-85) REVERT: A 341 ILE cc_start: 0.8510 (mp) cc_final: 0.8224 (mm) REVERT: L 49 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8303 (tptm) REVERT: L 182 THR cc_start: 0.8103 (m) cc_final: 0.7611 (t) REVERT: H 16 GLN cc_start: 0.8277 (mt0) cc_final: 0.7983 (mt0) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.5564 time to fit residues: 62.7731 Evaluate side-chains 108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.163165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113295 restraints weight = 12600.383| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.08 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7014 Z= 0.137 Angle : 0.557 10.499 9565 Z= 0.286 Chirality : 0.041 0.195 1124 Planarity : 0.005 0.047 1176 Dihedral : 7.548 66.160 984 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.13 % Allowed : 17.71 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.45 (0.29), residues: 879 helix: 2.68 (0.25), residues: 393 sheet: 1.68 (0.36), residues: 212 loop : -0.01 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 112 TYR 0.024 0.002 TYR H 78 PHE 0.011 0.001 PHE A 295 TRP 0.018 0.001 TRP H 34 HIS 0.009 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7005) covalent geometry : angle 0.55543 / 0.29 ( 9547) SS BOND : bond 0.00583 / 0.37 ( 9) SS BOND : angle 1.19064 / 0.65 ( 18) hydrogen bonds : bond 0.05400 / 3.63 ( 450) hydrogen bonds : angle 4.12460 / 2.99 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8403 (tttt) REVERT: A 296 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8031 (mtt-85) REVERT: A 341 ILE cc_start: 0.8543 (mp) cc_final: 0.8264 (mm) REVERT: L 49 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8347 (tptm) REVERT: L 182 THR cc_start: 0.8104 (m) cc_final: 0.7627 (t) REVERT: H 16 GLN cc_start: 0.8268 (mt0) cc_final: 0.7935 (mt0) outliers start: 16 outliers final: 16 residues processed: 106 average time/residue: 0.5694 time to fit residues: 63.5510 Evaluate side-chains 111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111610 restraints weight = 10593.160| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.92 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7014 Z= 0.192 Angle : 0.616 10.806 9565 Z= 0.318 Chirality : 0.044 0.221 1124 Planarity : 0.005 0.050 1176 Dihedral : 7.808 69.783 984 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 17.44 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.22 (0.29), residues: 879 helix: 2.42 (0.25), residues: 393 sheet: 1.63 (0.36), residues: 212 loop : -0.07 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 112 TYR 0.026 0.002 TYR H 78 PHE 0.013 0.002 PHE A 295 TRP 0.023 0.002 TRP H 34 HIS 0.010 0.001 HIS L 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 7005) covalent geometry : angle 0.61327 / 0.32 ( 9547) SS BOND : bond 0.00743 / 0.48 ( 9) SS BOND : angle 1.43601 / 0.81 ( 18) hydrogen bonds : bond 0.06321 / 4.25 ( 450) hydrogen bonds : angle 4.32552 / 3.13 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.90 seconds wall clock time: 68 minutes 10.56 seconds (4090.56 seconds total)