Starting phenix.real_space_refine on Thu Sep 18 19:26:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvn_47212/09_2025/9dvn_47212_trim.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 42 5.16 5 C 6476 2.51 5 N 1573 2.21 5 O 1770 1.98 5 H 9521 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19422 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9499 Classifications: {'peptide': 571} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 551} Chain breaks: 4 Chain: "B" Number of atoms: 9555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 9555 Classifications: {'peptide': 574} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain breaks: 4 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.22 Number of scatterers: 19422 At special positions: 0 Unit cell: (107.3, 93.525, 122.525, 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) S 42 16.00 P 40 15.00 O 1770 8.00 N 1573 7.00 C 6476 6.00 H 9521 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 502.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.646A pdb=" N HIS A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.264A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 47 through 98 Processing helix chain 'A' and resid 126 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.543A pdb=" N ALA A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.466A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.607A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 419 removed outlier: 5.887A pdb=" N VAL A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 445 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.034A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 582 removed outlier: 3.902A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.284A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 47 through 98 Processing helix chain 'B' and resid 123 through 168 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.543A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.730A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.321A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 267 through 296 removed outlier: 5.225A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.542A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.255A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.274A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.114A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix 734 hydrogen bonds defined for protein. 2169 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: 5.16 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9501 1.03 - 1.23: 30 1.23 - 1.43: 4375 1.43 - 1.62: 5709 1.62 - 1.82: 81 Bond restraints: 19696 Sorted by residual: bond pdb=" O45 I8P B 805 " pdb=" PB5 I8P B 805 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O45 I8P B 804 " pdb=" PB5 I8P B 804 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O45 I8P A 805 " pdb=" PB5 I8P A 805 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" O45 I8P A 804 " pdb=" PB5 I8P A 804 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" O3P CPL B 807 " pdb=" P CPL B 807 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 19691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 35093 3.04 - 6.09: 157 6.09 - 9.13: 71 9.13 - 12.17: 22 12.17 - 15.22: 18 Bond angle restraints: 35361 Sorted by residual: angle pdb=" O1P CPL B 807 " pdb=" P CPL B 807 " pdb=" O2P CPL B 807 " ideal model delta sigma weight residual 119.55 134.77 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O1P CPL A 807 " pdb=" P CPL A 807 " pdb=" O2P CPL A 807 " ideal model delta sigma weight residual 119.55 134.75 -15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O65 I8P A 804 " pdb=" PB5 I8P A 804 " pdb=" O75 I8P A 804 " ideal model delta sigma weight residual 113.85 99.79 14.06 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O65 I8P B 804 " pdb=" PB5 I8P B 804 " pdb=" O75 I8P B 804 " ideal model delta sigma weight residual 113.85 99.80 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O65 I8P A 805 " pdb=" PB5 I8P A 805 " pdb=" O75 I8P A 805 " ideal model delta sigma weight residual 113.85 99.86 13.99 3.00e+00 1.11e-01 2.17e+01 ... (remaining 35356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 9163 34.68 - 69.36: 388 69.36 - 104.04: 23 104.04 - 138.72: 10 138.72 - 173.40: 5 Dihedral angle restraints: 9589 sinusoidal: 5178 harmonic: 4411 Sorted by residual: dihedral pdb=" O35 I8P B 805 " pdb=" O45 I8P B 805 " pdb=" PA5 I8P B 805 " pdb=" PB5 I8P B 805 " ideal model delta sinusoidal sigma weight residual -10.77 162.63 -173.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 I8P A 804 " pdb=" O11 I8P A 804 " pdb=" PA1 I8P A 804 " pdb=" O41 I8P A 804 " ideal model delta sinusoidal sigma weight residual 309.75 162.66 147.09 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 CPL A 807 " pdb=" C1 CPL A 807 " pdb=" C2 CPL A 807 " pdb=" O3P CPL A 807 " ideal model delta sinusoidal sigma weight residual 72.09 -73.55 145.64 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 9586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1356 0.072 - 0.144: 112 0.144 - 0.216: 7 0.216 - 0.288: 3 0.288 - 0.360: 8 Chirality restraints: 1486 Sorted by residual: chirality pdb=" C17 CLR B 806 " pdb=" C13 CLR B 806 " pdb=" C16 CLR B 806 " pdb=" C20 CLR B 806 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C17 CLR A 806 " pdb=" C13 CLR A 806 " pdb=" C16 CLR A 806 " pdb=" C20 CLR A 806 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2 CPL A 807 " pdb=" C1 CPL A 807 " pdb=" C3 CPL A 807 " pdb=" O2 CPL A 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1483 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 604 " -0.002 9.50e-02 1.11e+02 1.48e-01 4.93e+02 pdb=" NE ARG B 604 " 0.187 2.00e-02 2.50e+03 pdb=" CZ ARG B 604 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARG B 604 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 604 " -0.014 2.00e-02 2.50e+03 pdb="HH11 ARG B 604 " -0.195 2.00e-02 2.50e+03 pdb="HH12 ARG B 604 " 0.062 2.00e-02 2.50e+03 pdb="HH21 ARG B 604 " -0.280 2.00e-02 2.50e+03 pdb="HH22 ARG B 604 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 604 " -0.175 9.50e-02 1.11e+02 1.19e-01 2.47e+02 pdb=" NE ARG A 604 " -0.130 2.00e-02 2.50e+03 pdb=" CZ ARG A 604 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 604 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 604 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 604 " 0.191 2.00e-02 2.50e+03 pdb="HH12 ARG A 604 " -0.117 2.00e-02 2.50e+03 pdb="HH21 ARG A 604 " 0.152 2.00e-02 2.50e+03 pdb="HH22 ARG A 604 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 482 " -0.013 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" N TYR A 483 " 0.042 2.00e-02 2.50e+03 pdb=" CA TYR A 483 " -0.011 2.00e-02 2.50e+03 pdb=" H TYR A 483 " -0.018 2.00e-02 2.50e+03 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1281 2.20 - 2.80: 39347 2.80 - 3.40: 56339 3.40 - 4.00: 71585 4.00 - 4.60: 110148 Nonbonded interactions: 278700 Sorted by model distance: nonbonded pdb=" O THR A 203 " pdb=" H GLY A 209 " model vdw 1.605 2.450 nonbonded pdb=" O ILE B 271 " pdb=" HH TYR B 352 " model vdw 1.616 2.450 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.622 2.450 nonbonded pdb="HH12 ARG A 270 " pdb=" O2 PO4 A 803 " model vdw 1.635 2.450 nonbonded pdb=" OD1 ASP A 566 " pdb="HH11 ARG A 603 " model vdw 1.637 2.450 ... (remaining 278695 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 1 through 98 or (resid 125 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name HA or name HB2 or name HB3)) or resid 126 through 157 or (resid 158 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2)) o \ r resid 159 through 807)) selection = (chain 'B' and (resid 1 through 98 or (resid 125 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name HA or name HB2 or name HB3)) or resid 126 through 807)) } 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: 5.500 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: 0.070 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 0.111 10177 Z= 0.302 Angle : 1.050 15.215 13842 Z= 0.402 Chirality : 0.046 0.360 1486 Planarity : 0.004 0.112 1653 Dihedral : 19.741 173.403 3970 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.99 % Allowed : 17.71 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.26), residues: 1125 helix: 3.39 (0.17), residues: 867 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 604 TYR 0.007 0.001 TYR A 518 PHE 0.022 0.001 PHE B 3 TRP 0.007 0.001 TRP B 327 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00598 (10175) covalent geometry : angle 1.05026 (13838) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.61141 ( 4) hydrogen bonds : bond 0.10473 ( 734) hydrogen bonds : angle 4.71129 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 582 THR cc_start: 0.6376 (p) cc_final: 0.5982 (p) REVERT: A 613 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: B 11 ILE cc_start: 0.7956 (mt) cc_final: 0.7326 (pt) REVERT: B 129 LYS cc_start: 0.6615 (mttt) cc_final: 0.6150 (tttt) REVERT: B 213 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6517 (tttt) REVERT: B 283 PHE cc_start: 0.7913 (t80) cc_final: 0.7550 (m-80) REVERT: B 394 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 417 TYR cc_start: 0.7188 (t80) cc_final: 0.6019 (m-80) outliers start: 10 outliers final: 2 residues processed: 122 average time/residue: 1.2749 time to fit residues: 167.5875 Evaluate side-chains 78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0370 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 476 HIS B 21 GLN B 476 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.210302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152364 restraints weight = 25158.938| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.65 r_work: 0.3512 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10177 Z= 0.158 Angle : 0.531 7.621 13842 Z= 0.274 Chirality : 0.036 0.187 1486 Planarity : 0.004 0.043 1653 Dihedral : 16.953 168.566 1745 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.68 % Allowed : 17.80 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.50 (0.25), residues: 1125 helix: 3.28 (0.16), residues: 856 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 604 TYR 0.012 0.002 TYR B 272 PHE 0.022 0.002 PHE A 605 TRP 0.010 0.001 TRP B 528 HIS 0.004 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00336 (10175) covalent geometry : angle 0.53093 (13838) SS BOND : bond 0.00515 ( 2) SS BOND : angle 1.34816 ( 4) hydrogen bonds : bond 0.04819 ( 734) hydrogen bonds : angle 4.24528 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7120 (mtmm) REVERT: B 11 ILE cc_start: 0.7878 (mt) cc_final: 0.7032 (pt) REVERT: B 129 LYS cc_start: 0.6274 (mttt) cc_final: 0.5789 (tttt) REVERT: B 213 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6297 (tttt) REVERT: B 394 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 417 TYR cc_start: 0.7417 (t80) cc_final: 0.6036 (m-80) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 1.3000 time to fit residues: 141.3652 Evaluate side-chains 86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.202245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138267 restraints weight = 25114.830| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.46 r_work: 0.3384 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10177 Z= 0.147 Angle : 0.511 7.731 13842 Z= 0.267 Chirality : 0.035 0.166 1486 Planarity : 0.004 0.044 1653 Dihedral : 15.646 166.378 1740 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.37 % Allowed : 15.73 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.25), residues: 1125 helix: 3.04 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 604 TYR 0.016 0.002 TYR A 352 PHE 0.027 0.002 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.006 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00314 (10175) covalent geometry : angle 0.51079 (13838) SS BOND : bond 0.00585 ( 2) SS BOND : angle 1.41084 ( 4) hydrogen bonds : bond 0.04921 ( 734) hydrogen bonds : angle 4.09127 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: A 405 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7896 (t) REVERT: B 129 LYS cc_start: 0.6299 (mttt) cc_final: 0.5764 (tttt) REVERT: B 394 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 417 TYR cc_start: 0.7649 (t80) cc_final: 0.6187 (m-80) REVERT: B 472 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7973 (mtp85) REVERT: B 575 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7623 (mm) outliers start: 24 outliers final: 10 residues processed: 101 average time/residue: 1.1727 time to fit residues: 128.7762 Evaluate side-chains 92 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 401 ASN A 576 GLN B 152 ASN B 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.202700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145725 restraints weight = 24910.713| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.57 r_work: 0.3411 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10177 Z= 0.216 Angle : 0.574 7.995 13842 Z= 0.304 Chirality : 0.038 0.214 1486 Planarity : 0.005 0.041 1653 Dihedral : 15.801 159.968 1740 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.57 % Allowed : 14.94 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.25), residues: 1125 helix: 2.66 (0.16), residues: 873 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 604 TYR 0.015 0.002 TYR B 272 PHE 0.029 0.002 PHE B 605 TRP 0.013 0.002 TRP B 514 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00497 (10175) covalent geometry : angle 0.57332 (13838) SS BOND : bond 0.00878 ( 2) SS BOND : angle 1.84032 ( 4) hydrogen bonds : bond 0.05692 ( 734) hydrogen bonds : angle 4.28572 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7624 (mttp) REVERT: A 137 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: A 318 GLU cc_start: 0.8226 (tt0) cc_final: 0.7987 (tt0) REVERT: A 398 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: A 405 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.7999 (t) REVERT: A 512 TYR cc_start: 0.7645 (m-10) cc_final: 0.7260 (m-10) REVERT: A 549 GLU cc_start: 0.7961 (pt0) cc_final: 0.7755 (pt0) REVERT: A 579 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7907 (mp) REVERT: B 129 LYS cc_start: 0.6383 (mttt) cc_final: 0.5883 (tttt) REVERT: B 213 LYS cc_start: 0.7622 (tppt) cc_final: 0.6629 (tttt) REVERT: B 216 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7637 (tttm) REVERT: B 394 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8346 (t80) REVERT: B 417 TYR cc_start: 0.7740 (t80) cc_final: 0.6470 (m-80) REVERT: B 472 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.8168 (mtp85) outliers start: 26 outliers final: 14 residues processed: 103 average time/residue: 1.3314 time to fit residues: 147.6057 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.205508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147873 restraints weight = 24992.741| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.58 r_work: 0.3443 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10177 Z= 0.137 Angle : 0.494 8.020 13842 Z= 0.261 Chirality : 0.034 0.188 1486 Planarity : 0.004 0.049 1653 Dihedral : 15.025 154.810 1740 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.08 % Allowed : 16.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.25), residues: 1125 helix: 2.89 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.38 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.010 0.001 TYR A 352 PHE 0.024 0.002 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00296 (10175) covalent geometry : angle 0.49322 (13838) SS BOND : bond 0.00594 ( 2) SS BOND : angle 1.88312 ( 4) hydrogen bonds : bond 0.04764 ( 734) hydrogen bonds : angle 4.11580 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7711 (mttp) REVERT: A 137 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: A 405 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 472 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.8056 (mtp-110) REVERT: A 512 TYR cc_start: 0.7624 (m-10) cc_final: 0.7216 (m-10) REVERT: A 549 GLU cc_start: 0.7934 (pt0) cc_final: 0.7707 (pt0) REVERT: B 129 LYS cc_start: 0.6345 (mttt) cc_final: 0.5877 (tttt) REVERT: B 213 LYS cc_start: 0.7584 (tppt) cc_final: 0.6630 (tttt) REVERT: B 216 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7565 (tttm) REVERT: B 394 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 472 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8138 (mtp85) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 1.0874 time to fit residues: 113.6972 Evaluate side-chains 86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.201841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144304 restraints weight = 24831.259| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.64 r_work: 0.3412 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10177 Z= 0.194 Angle : 0.542 8.393 13842 Z= 0.287 Chirality : 0.036 0.199 1486 Planarity : 0.004 0.048 1653 Dihedral : 15.073 148.447 1740 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.27 % Allowed : 15.63 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.25), residues: 1125 helix: 2.71 (0.16), residues: 871 sheet: None (None), residues: 0 loop : -1.45 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 604 TYR 0.013 0.002 TYR B 272 PHE 0.029 0.002 PHE A 605 TRP 0.013 0.002 TRP B 514 HIS 0.005 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00436 (10175) covalent geometry : angle 0.54110 (13838) SS BOND : bond 0.01042 ( 2) SS BOND : angle 2.20375 ( 4) hydrogen bonds : bond 0.05450 ( 734) hydrogen bonds : angle 4.19643 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: A 318 GLU cc_start: 0.8197 (tt0) cc_final: 0.7989 (tt0) REVERT: A 398 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: A 405 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7946 (t) REVERT: A 472 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7995 (mtp-110) REVERT: A 512 TYR cc_start: 0.7713 (m-10) cc_final: 0.7227 (m-80) REVERT: A 579 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 129 LYS cc_start: 0.6301 (mttt) cc_final: 0.5845 (tttt) REVERT: B 213 LYS cc_start: 0.7652 (tppt) cc_final: 0.6695 (tttt) REVERT: B 216 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7650 (ttpp) REVERT: B 394 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 472 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8161 (mtp85) outliers start: 23 outliers final: 14 residues processed: 94 average time/residue: 1.1673 time to fit residues: 119.0902 Evaluate side-chains 91 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147127 restraints weight = 24960.917| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.63 r_work: 0.3438 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10177 Z= 0.142 Angle : 0.496 8.296 13842 Z= 0.262 Chirality : 0.034 0.197 1486 Planarity : 0.004 0.039 1653 Dihedral : 14.387 142.638 1740 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 15.33 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.00 (0.25), residues: 1125 helix: 2.88 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.010 0.001 TYR B 352 PHE 0.025 0.002 PHE A 605 TRP 0.013 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00309 (10175) covalent geometry : angle 0.49504 (13838) SS BOND : bond 0.00635 ( 2) SS BOND : angle 1.70929 ( 4) hydrogen bonds : bond 0.04791 ( 734) hydrogen bonds : angle 4.09188 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: A 405 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 512 TYR cc_start: 0.7682 (m-10) cc_final: 0.7200 (m-10) REVERT: A 549 GLU cc_start: 0.7936 (pt0) cc_final: 0.7728 (pt0) REVERT: A 575 ILE cc_start: 0.8308 (mt) cc_final: 0.7955 (tp) REVERT: B 23 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6093 (mp0) REVERT: B 90 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7297 (mp0) REVERT: B 129 LYS cc_start: 0.6320 (mttt) cc_final: 0.5892 (tttt) REVERT: B 213 LYS cc_start: 0.7683 (tppt) cc_final: 0.6729 (tttt) REVERT: B 216 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7734 (ttpp) REVERT: B 394 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8530 (t80) REVERT: B 508 MET cc_start: 0.7083 (mmp) cc_final: 0.6132 (tpp) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 1.0984 time to fit residues: 114.8399 Evaluate side-chains 96 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.204367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150701 restraints weight = 24950.136| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.65 r_work: 0.3474 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10177 Z= 0.125 Angle : 0.484 8.506 13842 Z= 0.255 Chirality : 0.034 0.198 1486 Planarity : 0.004 0.110 1653 Dihedral : 13.868 139.590 1740 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 15.83 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.25), residues: 1125 helix: 3.03 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 472 TYR 0.010 0.001 TYR A 352 PHE 0.025 0.001 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00266 (10175) covalent geometry : angle 0.48369 (13838) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.55923 ( 4) hydrogen bonds : bond 0.04541 ( 734) hydrogen bonds : angle 4.00155 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 405 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7883 (t) REVERT: A 512 TYR cc_start: 0.7649 (m-10) cc_final: 0.7209 (m-10) REVERT: A 549 GLU cc_start: 0.7877 (pt0) cc_final: 0.7670 (pt0) REVERT: A 575 ILE cc_start: 0.8302 (mt) cc_final: 0.7954 (tp) REVERT: B 23 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6138 (mp0) REVERT: B 90 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7277 (mp0) REVERT: B 129 LYS cc_start: 0.6238 (mttt) cc_final: 0.5808 (tttt) REVERT: B 213 LYS cc_start: 0.7707 (tppt) cc_final: 0.6751 (tttt) REVERT: B 216 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7717 (ttpp) REVERT: B 394 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8517 (t80) REVERT: B 417 TYR cc_start: 0.7829 (t80) cc_final: 0.6486 (m-80) REVERT: B 508 MET cc_start: 0.7063 (mmp) cc_final: 0.6143 (tpp) outliers start: 19 outliers final: 12 residues processed: 95 average time/residue: 1.0312 time to fit residues: 106.2834 Evaluate side-chains 93 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.203185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149156 restraints weight = 24799.405| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.57 r_work: 0.3449 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10177 Z= 0.142 Angle : 0.496 8.488 13842 Z= 0.262 Chirality : 0.034 0.198 1486 Planarity : 0.004 0.036 1653 Dihedral : 13.762 136.652 1740 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.78 % Allowed : 15.83 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.25), residues: 1125 helix: 2.98 (0.16), residues: 871 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.010 0.001 TYR B 352 PHE 0.027 0.002 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00311 (10175) covalent geometry : angle 0.49532 (13838) SS BOND : bond 0.00653 ( 2) SS BOND : angle 1.49144 ( 4) hydrogen bonds : bond 0.04788 ( 734) hydrogen bonds : angle 4.02771 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: A 405 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (t) REVERT: A 575 ILE cc_start: 0.8331 (mt) cc_final: 0.7966 (tp) REVERT: B 23 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6184 (mp0) REVERT: B 90 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7278 (mp0) REVERT: B 129 LYS cc_start: 0.6152 (mttt) cc_final: 0.5733 (tttt) REVERT: B 213 LYS cc_start: 0.7663 (tppt) cc_final: 0.6695 (tttt) REVERT: B 216 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7686 (ttpp) REVERT: B 394 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 417 TYR cc_start: 0.7836 (t80) cc_final: 0.6482 (m-80) REVERT: B 508 MET cc_start: 0.7081 (mmp) cc_final: 0.5983 (tpp) REVERT: B 512 TYR cc_start: 0.7807 (m-10) cc_final: 0.7346 (m-10) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 1.0123 time to fit residues: 104.2306 Evaluate side-chains 93 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.203398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147513 restraints weight = 24999.225| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.56 r_work: 0.3453 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10177 Z= 0.134 Angle : 0.491 8.526 13842 Z= 0.259 Chirality : 0.034 0.197 1486 Planarity : 0.004 0.035 1653 Dihedral : 13.526 133.875 1740 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.68 % Allowed : 15.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.25), residues: 1125 helix: 2.98 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.010 0.001 TYR A 352 PHE 0.025 0.002 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00288 (10175) covalent geometry : angle 0.49003 (13838) SS BOND : bond 0.00617 ( 2) SS BOND : angle 1.49458 ( 4) hydrogen bonds : bond 0.04646 ( 734) hydrogen bonds : angle 4.00722 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: A 575 ILE cc_start: 0.8289 (mt) cc_final: 0.7931 (tp) REVERT: B 23 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6308 (mp0) REVERT: B 129 LYS cc_start: 0.6245 (mttt) cc_final: 0.5840 (tttt) REVERT: B 213 LYS cc_start: 0.7731 (tppt) cc_final: 0.6756 (tttt) REVERT: B 394 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8536 (t80) REVERT: B 417 TYR cc_start: 0.7864 (t80) cc_final: 0.6501 (m-80) REVERT: B 508 MET cc_start: 0.7063 (mmp) cc_final: 0.5981 (tpp) REVERT: B 512 TYR cc_start: 0.7810 (m-10) cc_final: 0.7539 (m-80) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 1.0543 time to fit residues: 107.6684 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.201855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141144 restraints weight = 25033.987| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.35 r_work: 0.3476 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10177 Z= 0.128 Angle : 0.490 8.515 13842 Z= 0.258 Chirality : 0.034 0.195 1486 Planarity : 0.004 0.049 1653 Dihedral : 13.381 132.501 1740 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.78 % Allowed : 15.83 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.21 (0.25), residues: 1125 helix: 3.00 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.010 0.001 TYR A 352 PHE 0.025 0.002 PHE A 605 TRP 0.012 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00274 (10175) covalent geometry : angle 0.48932 (13838) SS BOND : bond 0.00606 ( 2) SS BOND : angle 1.46682 ( 4) hydrogen bonds : bond 0.04569 ( 734) hydrogen bonds : angle 3.98522 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6605.25 seconds wall clock time: 112 minutes 34.38 seconds (6754.38 seconds total)