Starting phenix.real_space_refine on Wed Feb 12 10:29:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.map" model { file = "/net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfk_25091/02_2025/7sfk_25091.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.202 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4971 2.51 5 N 1098 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7419 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PEE': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 5, 'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 164 Unusual residues: {'PEE': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Restraints were copied for chains: B Time building chain proxies: 5.68, per 1000 atoms: 0.77 Number of scatterers: 7419 At special positions: 0 Unit cell: (78.453, 79.59, 88.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1299 8.00 N 1098 7.00 C 4971 6.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 962.9 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.510A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Proline residue: A 121 - end of helix removed outlier: 3.610A pdb=" N GLN A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 158 removed outlier: 3.832A pdb=" N CYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 200 removed outlier: 4.025A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 241 through 269 removed outlier: 3.601A pdb=" N GLU A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.705A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.511A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 3.610A pdb=" N GLN B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 158 removed outlier: 3.831A pdb=" N CYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 200 removed outlier: 4.026A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 241 through 269 removed outlier: 3.600A pdb=" N GLU B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.706A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 95 removed outlier: 3.510A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Proline residue: C 121 - end of helix removed outlier: 3.610A pdb=" N GLN C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 158 removed outlier: 3.832A pdb=" N CYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 200 removed outlier: 4.025A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 241 through 269 removed outlier: 3.600A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.706A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1323 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: 2.00 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2059 1.34 - 1.45: 1517 1.45 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 7572 Sorted by residual: bond pdb=" C30 PEE B 404 " pdb=" O5 PEE B 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE A 404 " pdb=" O5 PEE A 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE C 405 " pdb=" O5 PEE C 405 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE B 402 " pdb=" O5 PEE B 402 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE C 403 " pdb=" O5 PEE C 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.33e+01 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 9808 2.45 - 4.90: 315 4.90 - 7.34: 20 7.34 - 9.79: 15 9.79 - 12.24: 9 Bond angle restraints: 10167 Sorted by residual: angle pdb=" C11 PEE C 402 " pdb=" C10 PEE C 402 " pdb=" O2 PEE C 402 " ideal model delta sigma weight residual 111.70 123.94 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 123.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 111.70 123.92 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C31 PEE B 404 " pdb=" C30 PEE B 404 " pdb=" O3 PEE B 404 " ideal model delta sigma weight residual 111.87 123.95 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C31 PEE A 404 " pdb=" C30 PEE A 404 " pdb=" O3 PEE A 404 " ideal model delta sigma weight residual 111.87 123.91 -12.04 3.00e+00 1.11e-01 1.61e+01 ... (remaining 10162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 4197 35.68 - 71.36: 99 71.36 - 107.04: 12 107.04 - 142.72: 6 142.72 - 178.40: 6 Dihedral angle restraints: 4320 sinusoidal: 1845 harmonic: 2475 Sorted by residual: dihedral pdb=" C32 PEE C 404 " pdb=" C30 PEE C 404 " pdb=" C31 PEE C 404 " pdb=" O3 PEE C 404 " ideal model delta sinusoidal sigma weight residual 161.16 -20.44 -178.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE B 403 " pdb=" C30 PEE B 403 " pdb=" C31 PEE B 403 " pdb=" O3 PEE B 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.49 -178.35 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE A 403 " pdb=" C30 PEE A 403 " pdb=" C31 PEE A 403 " pdb=" O3 PEE A 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.54 -178.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 633 0.033 - 0.065: 282 0.065 - 0.098: 78 0.098 - 0.130: 15 0.130 - 0.163: 3 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C2 PEE A 406 " pdb=" C1 PEE A 406 " pdb=" C3 PEE A 406 " pdb=" O2 PEE A 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" C2 PEE B 406 " pdb=" C1 PEE B 406 " pdb=" C3 PEE B 406 " pdb=" O2 PEE B 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" C2 PEE C 408 " pdb=" C1 PEE C 408 " pdb=" C3 PEE C 408 " pdb=" O2 PEE C 408 " both_signs ideal model delta sigma weight residual False -2.33 -2.48 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1008 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 160 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 160 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 160 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 161 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 161 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 161 " -0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1868 2.79 - 3.32: 6599 3.32 - 3.85: 12571 3.85 - 4.37: 15095 4.37 - 4.90: 26074 Nonbonded interactions: 62207 Sorted by model distance: nonbonded pdb=" O GLY C 107 " pdb=" O HOH C 501 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 107 " pdb=" O HOH B 501 " model vdw 2.273 3.040 nonbonded pdb=" O GLY A 107 " pdb=" O HOH A 501 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" O HOH A 502 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" O HOH B 502 " model vdw 2.323 3.040 ... (remaining 62202 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'B' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'C' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or resid 406)) } 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=1.00 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: 0.460 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.760 Find NCS groups from input model: 0.350 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.008 0.147 7572 Z= 0.537 Angle : 0.966 12.239 10167 Z= 0.401 Chirality : 0.039 0.163 1011 Planarity : 0.005 0.050 1242 Dihedral : 18.398 178.399 2754 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.43 % Allowed : 1.71 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.28), residues: 843 helix: 1.80 (0.20), residues: 576 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.003 0.001 HIS B 96 PHE 0.016 0.001 PHE B 176 TYR 0.013 0.002 TYR B 271 ARG 0.002 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.751 Fit side-chains REVERT: A 68 GLN cc_start: 0.8415 (mp10) cc_final: 0.8188 (mp10) REVERT: A 148 MET cc_start: 0.7947 (ttp) cc_final: 0.7508 (ttp) REVERT: A 180 PHE cc_start: 0.8039 (t80) cc_final: 0.7823 (t80) REVERT: B 148 MET cc_start: 0.7888 (ttp) cc_final: 0.7637 (ttp) REVERT: C 148 MET cc_start: 0.8100 (ttp) cc_final: 0.7876 (ttp) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 1.0720 time to fit residues: 115.6276 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 192 GLN C 9 GLN C 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115420 restraints weight = 7059.854| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.17 r_work: 0.3053 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7572 Z= 0.270 Angle : 0.561 5.244 10167 Z= 0.299 Chirality : 0.042 0.126 1011 Planarity : 0.005 0.050 1242 Dihedral : 15.867 137.359 1301 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 5.84 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.29), residues: 843 helix: 2.00 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.55 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 19 HIS 0.006 0.001 HIS B 96 PHE 0.022 0.002 PHE C 155 TYR 0.026 0.002 TYR C 125 ARG 0.002 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.792 Fit side-chains REVERT: A 59 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7483 (mmtm) REVERT: A 68 GLN cc_start: 0.8206 (mp10) cc_final: 0.7641 (mp10) REVERT: A 117 MET cc_start: 0.8750 (mtt) cc_final: 0.8545 (mtt) REVERT: A 148 MET cc_start: 0.8461 (ttp) cc_final: 0.8153 (ttp) REVERT: A 221 MET cc_start: 0.7299 (tmm) cc_final: 0.6972 (tmm) REVERT: A 253 ASP cc_start: 0.8642 (m-30) cc_final: 0.8433 (m-30) REVERT: A 272 ASP cc_start: 0.7166 (p0) cc_final: 0.6893 (p0) REVERT: B 50 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: B 272 ASP cc_start: 0.7382 (p0) cc_final: 0.6987 (p0) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 1.1208 time to fit residues: 122.7851 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123552 restraints weight = 7130.907| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.03 r_work: 0.3147 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7572 Z= 0.155 Angle : 0.449 5.266 10167 Z= 0.239 Chirality : 0.037 0.122 1011 Planarity : 0.004 0.049 1242 Dihedral : 12.766 113.604 1301 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.00 % Allowed : 9.40 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.29), residues: 843 helix: 2.28 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 1.52 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 177 HIS 0.003 0.000 HIS B 96 PHE 0.012 0.001 PHE B 173 TYR 0.011 0.001 TYR A 271 ARG 0.002 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.749 Fit side-chains REVERT: A 59 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7455 (mmtm) REVERT: A 68 GLN cc_start: 0.8203 (mp10) cc_final: 0.7685 (mp10) REVERT: A 117 MET cc_start: 0.8747 (mtt) cc_final: 0.8529 (mtt) REVERT: A 148 MET cc_start: 0.8425 (ttp) cc_final: 0.8140 (ttp) REVERT: A 272 ASP cc_start: 0.7209 (p0) cc_final: 0.6953 (p0) REVERT: B 9 GLN cc_start: 0.8242 (tt0) cc_final: 0.7994 (tt0) REVERT: B 272 ASP cc_start: 0.7421 (p0) cc_final: 0.7068 (p0) REVERT: C 154 GLU cc_start: 0.8169 (tp30) cc_final: 0.7946 (tp30) REVERT: C 191 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7934 (tttm) outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 1.2130 time to fit residues: 128.7347 Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 221 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 78 ASN C 9 GLN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108307 restraints weight = 7312.913| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.19 r_work: 0.3127 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7572 Z= 0.328 Angle : 0.573 5.056 10167 Z= 0.305 Chirality : 0.043 0.127 1011 Planarity : 0.005 0.054 1242 Dihedral : 13.978 115.538 1299 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.14 % Allowed : 10.40 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.28), residues: 843 helix: 1.89 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.23 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 19 HIS 0.007 0.001 HIS A 96 PHE 0.029 0.002 PHE C 155 TYR 0.023 0.002 TYR A 271 ARG 0.003 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.692 Fit side-chains REVERT: A 59 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7482 (mmtm) REVERT: A 68 GLN cc_start: 0.8328 (mp10) cc_final: 0.7835 (mp10) REVERT: A 148 MET cc_start: 0.8514 (ttp) cc_final: 0.8186 (ttp) REVERT: A 272 ASP cc_start: 0.7408 (p0) cc_final: 0.7170 (p0) REVERT: B 9 GLN cc_start: 0.8320 (tt0) cc_final: 0.8011 (tt0) REVERT: B 272 ASP cc_start: 0.7736 (p0) cc_final: 0.7361 (p0) REVERT: C 221 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7064 (tmm) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 1.1760 time to fit residues: 134.5138 Evaluate side-chains 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 221 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110290 restraints weight = 7255.380| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.17 r_work: 0.3040 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7572 Z= 0.225 Angle : 0.503 5.121 10167 Z= 0.269 Chirality : 0.040 0.126 1011 Planarity : 0.005 0.053 1242 Dihedral : 13.013 114.361 1299 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.99 % Allowed : 10.83 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.28), residues: 843 helix: 2.01 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 1.25 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 19 HIS 0.005 0.001 HIS B 96 PHE 0.013 0.002 PHE A 155 TYR 0.016 0.002 TYR B 271 ARG 0.002 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.882 Fit side-chains REVERT: A 50 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: A 59 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7396 (mmtm) REVERT: A 68 GLN cc_start: 0.8192 (mp10) cc_final: 0.7762 (mp10) REVERT: A 148 MET cc_start: 0.8495 (ttp) cc_final: 0.8189 (ttp) REVERT: A 272 ASP cc_start: 0.7330 (p0) cc_final: 0.7105 (p0) REVERT: B 9 GLN cc_start: 0.8311 (tt0) cc_final: 0.8062 (tt0) REVERT: B 272 ASP cc_start: 0.7619 (p0) cc_final: 0.7268 (p0) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 1.1974 time to fit residues: 129.8155 Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110241 restraints weight = 7249.257| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.17 r_work: 0.3195 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7572 Z= 0.221 Angle : 0.499 5.248 10167 Z= 0.267 Chirality : 0.040 0.125 1011 Planarity : 0.005 0.053 1242 Dihedral : 12.824 114.399 1299 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.99 % Allowed : 12.11 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.28), residues: 843 helix: 2.05 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 1.23 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 19 HIS 0.004 0.001 HIS B 96 PHE 0.012 0.002 PHE B 173 TYR 0.016 0.002 TYR A 271 ARG 0.002 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.781 Fit side-chains REVERT: A 50 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: A 59 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7445 (mmtm) REVERT: A 68 GLN cc_start: 0.8244 (mp10) cc_final: 0.7675 (mp10) REVERT: A 148 MET cc_start: 0.8518 (ttp) cc_final: 0.8177 (ttp) REVERT: A 272 ASP cc_start: 0.7405 (p0) cc_final: 0.7179 (p0) REVERT: B 9 GLN cc_start: 0.8320 (tt0) cc_final: 0.8055 (tt0) REVERT: B 272 ASP cc_start: 0.7716 (p0) cc_final: 0.7364 (p0) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 1.0562 time to fit residues: 122.7051 Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109424 restraints weight = 7234.244| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.18 r_work: 0.3007 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7572 Z= 0.267 Angle : 0.532 5.238 10167 Z= 0.284 Chirality : 0.041 0.127 1011 Planarity : 0.005 0.054 1242 Dihedral : 13.247 114.799 1299 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.71 % Allowed : 12.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 843 helix: 1.98 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.08 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 19 HIS 0.005 0.001 HIS B 96 PHE 0.012 0.002 PHE C 219 TYR 0.019 0.002 TYR A 271 ARG 0.002 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.803 Fit side-chains REVERT: A 50 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 59 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7409 (mmtm) REVERT: A 68 GLN cc_start: 0.8141 (mp10) cc_final: 0.7522 (mp10) REVERT: A 148 MET cc_start: 0.8492 (ttp) cc_final: 0.8173 (ttp) REVERT: B 9 GLN cc_start: 0.8316 (tt0) cc_final: 0.8038 (tt0) REVERT: B 122 MET cc_start: 0.8417 (mtm) cc_final: 0.8120 (mtm) REVERT: B 272 ASP cc_start: 0.7641 (p0) cc_final: 0.7301 (p0) REVERT: C 70 GLU cc_start: 0.7695 (mp0) cc_final: 0.7067 (mp0) outliers start: 12 outliers final: 9 residues processed: 102 average time/residue: 1.1394 time to fit residues: 123.4864 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112929 restraints weight = 7254.235| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.13 r_work: 0.3047 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.003 0.032 7572 Z= 0.203 Angle : 0.487 5.246 10167 Z= 0.261 Chirality : 0.039 0.125 1011 Planarity : 0.004 0.053 1242 Dihedral : 12.691 114.438 1299 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.57 % Allowed : 13.11 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.28), residues: 843 helix: 2.06 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.19 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 19 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.002 PHE B 173 TYR 0.015 0.002 TYR A 271 ARG 0.001 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.788 Fit side-chains REVERT: A 68 GLN cc_start: 0.8006 (mp10) cc_final: 0.7493 (mp10) REVERT: A 148 MET cc_start: 0.8461 (ttp) cc_final: 0.8177 (ttp) REVERT: B 9 GLN cc_start: 0.8300 (tt0) cc_final: 0.8023 (tt0) REVERT: B 272 ASP cc_start: 0.7592 (p0) cc_final: 0.7254 (p0) REVERT: C 70 GLU cc_start: 0.7709 (mp0) cc_final: 0.7278 (mp0) outliers start: 11 outliers final: 10 residues processed: 103 average time/residue: 1.1701 time to fit residues: 128.1549 Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112762 restraints weight = 7298.356| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.14 r_work: 0.3058 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7572 Z= 0.201 Angle : 0.488 5.337 10167 Z= 0.262 Chirality : 0.039 0.126 1011 Planarity : 0.004 0.053 1242 Dihedral : 12.641 114.400 1299 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.71 % Allowed : 13.25 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.28), residues: 843 helix: 2.08 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.20 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 52 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.002 PHE A 173 TYR 0.014 0.002 TYR A 271 ARG 0.001 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.746 Fit side-chains REVERT: A 59 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7449 (mmtm) REVERT: A 68 GLN cc_start: 0.8084 (mp10) cc_final: 0.7578 (mp10) REVERT: A 148 MET cc_start: 0.8510 (ttp) cc_final: 0.8223 (ttp) REVERT: A 191 LYS cc_start: 0.8379 (tttm) cc_final: 0.8018 (tttm) REVERT: B 9 GLN cc_start: 0.8320 (tt0) cc_final: 0.8046 (tt0) REVERT: B 122 MET cc_start: 0.8309 (mtm) cc_final: 0.8026 (mtm) REVERT: B 272 ASP cc_start: 0.7672 (p0) cc_final: 0.7314 (p0) REVERT: C 70 GLU cc_start: 0.7748 (mp0) cc_final: 0.7302 (mp0) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 1.2683 time to fit residues: 135.8329 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111296 restraints weight = 7278.919| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.13 r_work: 0.3190 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7572 Z= 0.250 Angle : 0.519 5.290 10167 Z= 0.278 Chirality : 0.041 0.127 1011 Planarity : 0.005 0.054 1242 Dihedral : 12.967 114.784 1299 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 13.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.28), residues: 843 helix: 2.04 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.07 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 52 HIS 0.005 0.001 HIS B 96 PHE 0.012 0.002 PHE C 173 TYR 0.018 0.002 TYR B 271 ARG 0.002 0.000 ARG C 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.803 Fit side-chains REVERT: A 59 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7501 (mmtm) REVERT: A 68 GLN cc_start: 0.8251 (mp10) cc_final: 0.7647 (mp10) REVERT: A 148 MET cc_start: 0.8514 (ttp) cc_final: 0.8222 (ttp) REVERT: A 191 LYS cc_start: 0.8445 (tttm) cc_final: 0.8094 (tttm) REVERT: B 9 GLN cc_start: 0.8321 (tt0) cc_final: 0.8064 (tt0) REVERT: B 122 MET cc_start: 0.8409 (mtm) cc_final: 0.8130 (mtm) REVERT: B 272 ASP cc_start: 0.7791 (p0) cc_final: 0.7462 (p0) REVERT: C 70 GLU cc_start: 0.7807 (mp0) cc_final: 0.7357 (mp0) outliers start: 11 outliers final: 11 residues processed: 100 average time/residue: 1.1784 time to fit residues: 125.1661 Evaluate side-chains 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114414 restraints weight = 7183.984| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.11 r_work: 0.3055 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7572 Z= 0.169 Angle : 0.466 5.431 10167 Z= 0.250 Chirality : 0.038 0.124 1011 Planarity : 0.004 0.053 1242 Dihedral : 12.393 113.886 1299 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.85 % Allowed : 13.39 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.28), residues: 843 helix: 2.17 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.17 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 52 HIS 0.003 0.000 HIS A 96 PHE 0.011 0.001 PHE B 173 TYR 0.013 0.001 TYR A 271 ARG 0.001 0.000 ARG C 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.07 seconds wall clock time: 82 minutes 51.18 seconds (4971.18 seconds total)