Starting phenix.real_space_refine on Tue Jun 17 04:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvn_47212/06_2025/9dvn_47212_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvn_47212/06_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_47212/06_2025/9dvn_47212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvn_47212/06_2025/9dvn_47212.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvn_47212/06_2025/9dvn_47212_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvn_47212/06_2025/9dvn_47212_trim.cif" } resolution = 2.75 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= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.10, per 1000 atoms: 0.52 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: 5.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.20 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: 6.86 Time building geometry restraints manager: 6.48 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 625 or resid 801 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 625 or resid 801 thr \ ough 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: 3.530 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: 0.340 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 42.040 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.190 ------------------------------------------------------------------------------- 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 (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: 3.70 (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 TRP 0.007 0.001 TRP B 327 HIS 0.004 0.001 HIS A 387 PHE 0.022 0.001 PHE B 3 TYR 0.007 0.001 TYR A 518 ARG 0.010 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.10473 ( 734) hydrogen bonds : angle 4.71129 ( 2169) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.61141 ( 4) covalent geometry : bond 0.00598 (10175) covalent geometry : angle 1.05026 (13838) *********************** 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 : 1.462 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: 2.3425 time to fit residues: 310.4895 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 : 1.504 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.210024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151815 restraints weight = 24998.316| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.72 r_work: 0.3498 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10177 Z= 0.152 Angle : 0.537 7.378 13842 Z= 0.278 Chirality : 0.036 0.217 1486 Planarity : 0.004 0.048 1653 Dihedral : 16.766 168.574 1745 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.68 % Allowed : 17.71 % Favored : 80.61 % 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: 3.47 (0.25), residues: 1125 helix: 3.26 (0.16), residues: 856 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.004 0.001 HIS B 441 PHE 0.026 0.002 PHE A 605 TYR 0.012 0.002 TYR B 272 ARG 0.016 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 734) hydrogen bonds : angle 4.23807 ( 2169) SS BOND : bond 0.00516 ( 2) SS BOND : angle 1.41635 ( 4) covalent geometry : bond 0.00326 (10175) covalent geometry : angle 0.53663 (13838) *********************** 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 : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7208 (mtmm) REVERT: A 349 LEU cc_start: 0.8425 (tp) cc_final: 0.8201 (tp) REVERT: B 11 ILE cc_start: 0.7857 (mt) cc_final: 0.7012 (pt) REVERT: B 129 LYS cc_start: 0.6242 (mttt) cc_final: 0.5758 (tttt) REVERT: B 213 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6267 (tttt) REVERT: B 394 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 417 TYR cc_start: 0.7435 (t80) cc_final: 0.6044 (m-80) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 2.4960 time to fit residues: 274.1941 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 : 1.414 ------------------------------------------------------------------------------- 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 47 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.202832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144021 restraints weight = 24807.618| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.51 r_work: 0.3403 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10177 Z= 0.153 Angle : 0.517 7.825 13842 Z= 0.270 Chirality : 0.035 0.167 1486 Planarity : 0.004 0.041 1653 Dihedral : 15.693 165.759 1740 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.47 % Allowed : 15.63 % 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 (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: 3.19 (0.25), residues: 1125 helix: 3.00 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -1.33 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 514 HIS 0.006 0.001 HIS A 476 PHE 0.029 0.002 PHE A 605 TYR 0.015 0.002 TYR A 352 ARG 0.007 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 734) hydrogen bonds : angle 4.11814 ( 2169) SS BOND : bond 0.00604 ( 2) SS BOND : angle 1.39972 ( 4) covalent geometry : bond 0.00331 (10175) covalent geometry : angle 0.51686 (13838) *********************** 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 108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: A 405 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7939 (t) REVERT: B 129 LYS cc_start: 0.6349 (mttt) cc_final: 0.5813 (tttt) REVERT: B 394 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 417 TYR cc_start: 0.7664 (t80) cc_final: 0.6294 (m-80) REVERT: B 472 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.7999 (mtp85) outliers start: 25 outliers final: 10 residues processed: 102 average time/residue: 2.1939 time to fit residues: 244.1291 Evaluate side-chains 94 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 582 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 576 GLN B 152 ASN B 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.198883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136061 restraints weight = 25013.289| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.39 r_work: 0.3379 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10177 Z= 0.234 Angle : 0.616 8.089 13842 Z= 0.327 Chirality : 0.039 0.227 1486 Planarity : 0.005 0.044 1653 Dihedral : 15.900 157.002 1740 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.87 % Allowed : 14.34 % Favored : 82.79 % 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: 2.45 (0.24), residues: 1125 helix: 2.45 (0.16), residues: 870 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 514 HIS 0.006 0.001 HIS B 616 PHE 0.033 0.003 PHE B 605 TYR 0.018 0.002 TYR B 272 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06032 ( 734) hydrogen bonds : angle 4.38202 ( 2169) SS BOND : bond 0.00913 ( 2) SS BOND : angle 2.08957 ( 4) covalent geometry : bond 0.00532 (10175) covalent geometry : angle 0.61532 (13838) *********************** 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 114 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7521 (mttp) REVERT: A 137 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: A 318 GLU cc_start: 0.8317 (tt0) cc_final: 0.8038 (tt0) REVERT: A 398 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: A 405 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 508 MET cc_start: 0.7838 (mmp) cc_final: 0.7598 (mmp) REVERT: A 512 TYR cc_start: 0.7630 (m-10) cc_final: 0.7130 (m-10) REVERT: A 549 GLU cc_start: 0.8036 (pt0) cc_final: 0.7806 (pt0) REVERT: A 579 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 129 LYS cc_start: 0.6095 (mttt) cc_final: 0.5623 (tttt) REVERT: B 213 LYS cc_start: 0.7568 (tppt) cc_final: 0.6605 (tttt) REVERT: B 216 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7643 (ttpp) REVERT: B 394 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8348 (t80) REVERT: B 417 TYR cc_start: 0.7792 (t80) cc_final: 0.6488 (m-80) REVERT: B 472 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8120 (mtp85) outliers start: 29 outliers final: 16 residues processed: 105 average time/residue: 2.5450 time to fit residues: 289.1145 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 A 452 GLN A 576 GLN B 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.203338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145950 restraints weight = 24915.704| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.65 r_work: 0.3427 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3594 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= 0.153 Angle : 0.514 8.097 13842 Z= 0.273 Chirality : 0.035 0.186 1486 Planarity : 0.004 0.045 1653 Dihedral : 15.097 151.103 1740 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.37 % Allowed : 15.43 % Favored : 82.20 % 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: 2.75 (0.25), residues: 1125 helix: 2.69 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.45 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.027 0.002 PHE A 605 TYR 0.011 0.001 TYR A 352 ARG 0.004 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.05069 ( 734) hydrogen bonds : angle 4.20536 ( 2169) SS BOND : bond 0.00834 ( 2) SS BOND : angle 1.81827 ( 4) covalent geometry : bond 0.00334 (10175) covalent geometry : angle 0.51335 (13838) *********************** 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 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: A 318 GLU cc_start: 0.8229 (tt0) cc_final: 0.7925 (tt0) REVERT: A 405 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7900 (t) REVERT: A 508 MET cc_start: 0.7910 (mmp) cc_final: 0.7707 (mmp) REVERT: A 512 TYR cc_start: 0.7685 (m-10) cc_final: 0.7195 (m-80) REVERT: A 549 GLU cc_start: 0.8003 (pt0) cc_final: 0.7764 (pt0) REVERT: A 579 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 129 LYS cc_start: 0.6359 (mttt) cc_final: 0.5899 (tttt) REVERT: B 216 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7657 (ttpp) REVERT: B 394 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8447 (t80) REVERT: B 472 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8173 (mtp85) outliers start: 24 outliers final: 13 residues processed: 97 average time/residue: 2.2604 time to fit residues: 239.3450 Evaluate side-chains 92 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 130 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 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 95 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.201108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143638 restraints weight = 24839.990| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.62 r_work: 0.3408 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10177 Z= 0.197 Angle : 0.544 8.353 13842 Z= 0.288 Chirality : 0.036 0.202 1486 Planarity : 0.004 0.042 1653 Dihedral : 15.116 146.099 1740 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.37 % Allowed : 15.13 % 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 (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 (0.25), residues: 1125 helix: 2.60 (0.16), residues: 870 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 514 HIS 0.005 0.001 HIS A 476 PHE 0.029 0.002 PHE A 605 TYR 0.013 0.002 TYR B 272 ARG 0.005 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 734) hydrogen bonds : angle 4.24308 ( 2169) SS BOND : bond 0.00916 ( 2) SS BOND : angle 2.09310 ( 4) covalent geometry : bond 0.00443 (10175) covalent geometry : angle 0.54303 (13838) *********************** 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: 24 poor density : 76 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: A 318 GLU cc_start: 0.8327 (tt0) cc_final: 0.8098 (tt0) REVERT: A 398 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: A 405 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7910 (t) REVERT: A 512 TYR cc_start: 0.7716 (m-10) cc_final: 0.7218 (m-10) REVERT: A 579 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 23 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6155 (mp0) REVERT: B 90 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7205 (mp0) REVERT: B 129 LYS cc_start: 0.6394 (mttt) cc_final: 0.5956 (tttt) REVERT: B 213 LYS cc_start: 0.7731 (tppt) cc_final: 0.6801 (tttt) REVERT: B 216 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7729 (ttpp) REVERT: B 394 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8455 (t80) REVERT: B 508 MET cc_start: 0.7226 (mmp) cc_final: 0.6260 (tpp) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 2.3931 time to fit residues: 244.5340 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 : 1.356 ------------------------------------------------------------------------------- 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 130 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.202855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145155 restraints weight = 24824.017| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.55 r_work: 0.3423 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3880 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= 0.143 Angle : 0.501 8.334 13842 Z= 0.264 Chirality : 0.034 0.194 1486 Planarity : 0.004 0.037 1653 Dihedral : 14.478 141.248 1740 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.37 % Allowed : 15.13 % 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 (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: 2.90 (0.25), residues: 1125 helix: 2.81 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.026 0.002 PHE A 605 TYR 0.010 0.001 TYR B 352 ARG 0.003 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 734) hydrogen bonds : angle 4.12726 ( 2169) SS BOND : bond 0.00693 ( 2) SS BOND : angle 1.75942 ( 4) covalent geometry : bond 0.00307 (10175) covalent geometry : angle 0.50005 (13838) *********************** 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 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: A 318 GLU cc_start: 0.8263 (tt0) cc_final: 0.7915 (tt0) REVERT: A 405 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 512 TYR cc_start: 0.7666 (m-10) cc_final: 0.7216 (m-10) REVERT: A 549 GLU cc_start: 0.7976 (pt0) cc_final: 0.7709 (pt0) REVERT: A 575 ILE cc_start: 0.8327 (mt) cc_final: 0.7960 (tp) REVERT: B 23 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6183 (mp0) REVERT: B 90 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7241 (mp0) REVERT: B 129 LYS cc_start: 0.6326 (mttt) cc_final: 0.5899 (tttt) REVERT: B 213 LYS cc_start: 0.7666 (tppt) cc_final: 0.6718 (tttt) REVERT: B 216 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7633 (ttpp) REVERT: B 394 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 508 MET cc_start: 0.7170 (mmp) cc_final: 0.6219 (tpp) outliers start: 24 outliers final: 14 residues processed: 97 average time/residue: 2.2181 time to fit residues: 238.5031 Evaluate side-chains 91 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.202206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147570 restraints weight = 24817.421| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.62 r_work: 0.3431 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4010 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= 0.147 Angle : 0.506 8.474 13842 Z= 0.267 Chirality : 0.034 0.201 1486 Planarity : 0.004 0.048 1653 Dihedral : 14.272 137.883 1740 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 15.13 % Favored : 82.69 % 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: 2.98 (0.25), residues: 1125 helix: 2.86 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 514 HIS 0.005 0.001 HIS A 476 PHE 0.028 0.002 PHE A 605 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 734) hydrogen bonds : angle 4.09071 ( 2169) SS BOND : bond 0.00704 ( 2) SS BOND : angle 1.63235 ( 4) covalent geometry : bond 0.00322 (10175) covalent geometry : angle 0.50498 (13838) *********************** 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 102 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: A 318 GLU cc_start: 0.8246 (tt0) cc_final: 0.7930 (tt0) REVERT: A 405 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7881 (t) REVERT: A 549 GLU cc_start: 0.7994 (pt0) cc_final: 0.7766 (pt0) REVERT: A 575 ILE cc_start: 0.8281 (mt) cc_final: 0.7933 (tp) REVERT: B 23 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6234 (mp0) REVERT: B 129 LYS cc_start: 0.6226 (mttt) cc_final: 0.5795 (tttt) REVERT: B 213 LYS cc_start: 0.7756 (tppt) cc_final: 0.6786 (tttt) REVERT: B 216 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7677 (ttpp) REVERT: B 394 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8523 (t80) REVERT: B 417 TYR cc_start: 0.7842 (t80) cc_final: 0.6507 (m-80) REVERT: B 508 MET cc_start: 0.7157 (mmp) cc_final: 0.6217 (tpp) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 2.1318 time to fit residues: 226.2837 Evaluate side-chains 93 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.202190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147398 restraints weight = 24889.702| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.58 r_work: 0.3424 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10177 Z= 0.147 Angle : 0.508 8.478 13842 Z= 0.268 Chirality : 0.034 0.197 1486 Planarity : 0.004 0.035 1653 Dihedral : 14.091 135.637 1740 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 15.53 % 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 (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: 2.98 (0.25), residues: 1125 helix: 2.85 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.027 0.002 PHE A 605 TYR 0.010 0.001 TYR B 352 ARG 0.003 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 734) hydrogen bonds : angle 4.08499 ( 2169) SS BOND : bond 0.00686 ( 2) SS BOND : angle 1.67258 ( 4) covalent geometry : bond 0.00321 (10175) covalent geometry : angle 0.50707 (13838) *********************** 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 104 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: A 270 ARG cc_start: 0.8513 (mmt180) cc_final: 0.8266 (mmt180) REVERT: A 318 GLU cc_start: 0.8257 (tt0) cc_final: 0.7902 (tt0) REVERT: A 405 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 549 GLU cc_start: 0.7989 (pt0) cc_final: 0.7760 (pt0) REVERT: A 575 ILE cc_start: 0.8279 (mt) cc_final: 0.7929 (tp) REVERT: B 23 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6241 (mp0) REVERT: B 129 LYS cc_start: 0.6252 (mttt) cc_final: 0.5814 (tttt) REVERT: B 213 LYS cc_start: 0.7742 (tppt) cc_final: 0.6762 (tttt) REVERT: B 216 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7774 (ttpp) REVERT: B 394 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 417 TYR cc_start: 0.7846 (t80) cc_final: 0.6471 (m-80) REVERT: B 508 MET cc_start: 0.7152 (mmp) cc_final: 0.6026 (tpp) REVERT: B 512 TYR cc_start: 0.7842 (m-10) cc_final: 0.7424 (m-10) outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 2.1932 time to fit residues: 234.8636 Evaluate side-chains 97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.197847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141509 restraints weight = 24975.849| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.60 r_work: 0.3397 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10177 Z= 0.183 Angle : 0.540 8.606 13842 Z= 0.285 Chirality : 0.036 0.200 1486 Planarity : 0.004 0.038 1653 Dihedral : 14.390 133.154 1740 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 15.83 % Favored : 82.00 % 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 (0.25), residues: 1125 helix: 2.70 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -1.45 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 514 HIS 0.005 0.001 HIS A 476 PHE 0.029 0.002 PHE A 605 TYR 0.012 0.002 TYR B 272 ARG 0.004 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 734) hydrogen bonds : angle 4.16685 ( 2169) SS BOND : bond 0.00744 ( 2) SS BOND : angle 1.61405 ( 4) covalent geometry : bond 0.00414 (10175) covalent geometry : angle 0.53939 (13838) ********************** 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 102 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: A 318 GLU cc_start: 0.8266 (tt0) cc_final: 0.8024 (tt0) REVERT: A 405 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7924 (t) REVERT: A 549 GLU cc_start: 0.7974 (pt0) cc_final: 0.7703 (pt0) REVERT: A 575 ILE cc_start: 0.8310 (mt) cc_final: 0.7971 (tp) REVERT: B 23 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6376 (mp0) REVERT: B 129 LYS cc_start: 0.6244 (mttt) cc_final: 0.5820 (tttt) REVERT: B 193 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7133 (mt0) REVERT: B 213 LYS cc_start: 0.7816 (tppt) cc_final: 0.6845 (tttt) REVERT: B 216 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7764 (ttpp) REVERT: B 394 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8496 (t80) REVERT: B 417 TYR cc_start: 0.7838 (t80) cc_final: 0.6447 (m-80) REVERT: B 508 MET cc_start: 0.7200 (mmp) cc_final: 0.6163 (tpp) REVERT: B 512 TYR cc_start: 0.7803 (m-10) cc_final: 0.7517 (m-10) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 2.2555 time to fit residues: 238.9578 Evaluate side-chains 92 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.200973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145017 restraints weight = 25068.037| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.64 r_work: 0.3421 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4274 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= 0.142 Angle : 0.507 8.532 13842 Z= 0.268 Chirality : 0.034 0.191 1486 Planarity : 0.004 0.041 1653 Dihedral : 14.016 132.452 1740 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.98 % Allowed : 16.12 % 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 (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: 2.94 (0.25), residues: 1125 helix: 2.82 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.004 0.001 HIS A 476 PHE 0.026 0.002 PHE A 605 TYR 0.010 0.001 TYR B 352 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 734) hydrogen bonds : angle 4.08831 ( 2169) SS BOND : bond 0.00697 ( 2) SS BOND : angle 1.64676 ( 4) covalent geometry : bond 0.00310 (10175) covalent geometry : angle 0.50650 (13838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13028.21 seconds wall clock time: 220 minutes 51.28 seconds (13251.28 seconds total)