Starting phenix.real_space_refine on Thu Jul 2 19:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.map" model { file = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psn_13615/07_2026/7psn_13615.cif" } resolution = 2.9 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= -0.001 sd= 0.089 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 10 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6088 2.51 5 N 1604 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B Time building chain proxies: 2.76, per 1000 atoms: 0.29 Number of scatterers: 9464 At special positions: 0 Unit cell: (83.628, 75.348, 141.588, 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 34 16.00 P 10 15.00 Mg 2 11.99 O 1726 8.00 N 1604 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 300.8 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 68.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.747A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 233 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 367 removed outlier: 3.583A pdb=" N LEU A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.697A pdb=" N PHE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.593A pdb=" N ILE A 636 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.748A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 233 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 313 through 367 removed outlier: 3.584A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 396 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.696A pdb=" N PHE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.594A pdb=" N ILE B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 676 Processing sheet with id=AA1, first strand: chain 'A' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 457 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU A 439 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 459 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N THR A 437 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 441 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER A 490 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.528A pdb=" N MET A 594 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 629 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 596 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 641 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 642 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 653 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 644 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE B 457 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 439 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 459 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 437 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 441 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 490 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.529A pdb=" N MET B 594 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 629 " --> pdb=" O MET B 594 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 596 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 641 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 642 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 653 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 644 " --> pdb=" O ARG B 651 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.43: 2478 1.43 - 1.56: 5568 1.56 - 1.68: 14 1.68 - 1.80: 68 Bond restraints: 9636 Sorted by residual: bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.626 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.625 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C6 ANP A 701 " pdb=" N6 ANP A 701 " ideal model delta sigma weight residual 1.340 1.471 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 12846 2.77 - 5.54: 126 5.54 - 8.30: 28 8.30 - 11.07: 12 11.07 - 13.84: 8 Bond angle restraints: 13020 Sorted by residual: angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.54 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.59 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O3 LOP A 704 " pdb=" P1 LOP A 704 " pdb=" O4 LOP A 704 " ideal model delta sigma weight residual 120.67 109.29 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O3 LOP B 704 " pdb=" P1 LOP B 704 " pdb=" O4 LOP B 704 " ideal model delta sigma weight residual 120.67 109.32 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" O5' ANP A 701 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 5469 25.69 - 51.38: 267 51.38 - 77.07: 18 77.07 - 102.76: 0 102.76 - 128.44: 2 Dihedral angle restraints: 5756 sinusoidal: 2372 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.33 128.44 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.31 128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" CB MET B 199 " pdb=" CG MET B 199 " pdb=" SD MET B 199 " pdb=" CE MET B 199 " ideal model delta sinusoidal sigma weight residual 60.00 117.46 -57.46 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 5753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 408 0.072 - 0.108: 114 0.108 - 0.144: 14 0.144 - 0.180: 6 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ANP A 701 " pdb=" C1' ANP A 701 " pdb=" C3' ANP A 701 " pdb=" O2' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ANP B 701 " pdb=" C1' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O2' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C4 LOP A 704 " pdb=" C3 LOP A 704 " pdb=" C5 LOP A 704 " pdb=" O5 LOP A 704 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1493 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP B 703 " 0.204 2.00e-02 2.50e+03 2.05e-01 4.21e+02 pdb=" C14 LOP B 703 " -0.200 2.00e-02 2.50e+03 pdb=" C15 LOP B 703 " -0.210 2.00e-02 2.50e+03 pdb=" C16 LOP B 703 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 703 " -0.204 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C14 LOP A 703 " 0.200 2.00e-02 2.50e+03 pdb=" C15 LOP A 703 " 0.210 2.00e-02 2.50e+03 pdb=" C16 LOP A 703 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 387 " -0.005 2.00e-02 2.50e+03 8.91e-03 7.93e-01 pdb=" C VAL A 387 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 387 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.005 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 70 2.52 - 3.11: 7626 3.11 - 3.71: 14350 3.71 - 4.30: 20897 4.30 - 4.90: 35778 Nonbonded interactions: 78721 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN A 517 " pdb="MG MG A 702 " model vdw 1.923 2.170 nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.963 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.963 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.047 2.170 ... (remaining 78716 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.009 0.224 9636 Z= 0.404 Angle : 0.823 13.840 13020 Z= 0.365 Chirality : 0.042 0.180 1496 Planarity : 0.008 0.205 1620 Dihedral : 14.292 128.445 3572 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.21), residues: 1166 helix: -1.13 (0.16), residues: 772 sheet: -3.80 (0.43), residues: 52 loop : -3.49 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.011 0.002 TYR B 161 PHE 0.009 0.001 PHE A 179 TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00903 / 0.40 ( 9636) covalent geometry : angle 0.82288 / 0.37 (13020) hydrogen bonds : bond 0.11032 / 7.44 ( 634) hydrogen bonds : angle 5.29664 / 3.94 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.320 Fit side-chains REVERT: A 426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.5282 time to fit residues: 68.8565 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 304 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117993 restraints weight = 10387.191| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.14 r_work: 0.3318 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9636 Z= 0.134 Angle : 0.526 7.461 13020 Z= 0.271 Chirality : 0.040 0.150 1496 Planarity : 0.003 0.029 1620 Dihedral : 9.987 133.220 1374 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.80 % Allowed : 10.08 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1166 helix: 0.70 (0.18), residues: 780 sheet: -2.63 (0.50), residues: 62 loop : -2.61 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.014 0.001 TYR B 161 PHE 0.012 0.001 PHE A 391 TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9636) covalent geometry : angle 0.52552 / 0.27 (13020) hydrogen bonds : bond 0.04173 / 2.79 ( 634) hydrogen bonds : angle 3.80445 / 2.81 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.343 Fit side-chains REVERT: A 426 LEU cc_start: 0.8337 (mm) cc_final: 0.8098 (mp) outliers start: 8 outliers final: 2 residues processed: 117 average time/residue: 0.4766 time to fit residues: 60.1527 Evaluate side-chains 97 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 572 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113265 restraints weight = 10553.621| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.16 r_work: 0.3292 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9636 Z= 0.141 Angle : 0.524 7.402 13020 Z= 0.269 Chirality : 0.041 0.184 1496 Planarity : 0.003 0.033 1620 Dihedral : 9.133 126.313 1374 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.20 % Allowed : 13.57 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1166 helix: 1.24 (0.18), residues: 780 sheet: -2.23 (0.56), residues: 62 loop : -2.05 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.010 0.001 TYR B 161 PHE 0.014 0.001 PHE A 179 TRP 0.007 0.001 TRP B 100 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9636) covalent geometry : angle 0.52371 / 0.27 (13020) hydrogen bonds : bond 0.04198 / 2.82 ( 634) hydrogen bonds : angle 3.65845 / 2.72 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.354 Fit side-chains REVERT: A 581 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7069 (mp) REVERT: A 666 LEU cc_start: 0.6737 (tm) cc_final: 0.6498 (tm) REVERT: B 581 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7026 (mp) REVERT: B 666 LEU cc_start: 0.6763 (tm) cc_final: 0.6468 (tm) outliers start: 12 outliers final: 2 residues processed: 130 average time/residue: 0.4252 time to fit residues: 60.2569 Evaluate side-chains 106 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111432 restraints weight = 10904.059| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.08 r_work: 0.3207 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9636 Z= 0.156 Angle : 0.525 6.866 13020 Z= 0.269 Chirality : 0.041 0.152 1496 Planarity : 0.003 0.024 1620 Dihedral : 8.955 125.454 1374 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 14.67 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1166 helix: 1.38 (0.18), residues: 784 sheet: -2.00 (0.58), residues: 62 loop : -1.76 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 424 TYR 0.019 0.002 TYR A 161 PHE 0.023 0.001 PHE B 350 TRP 0.007 0.001 TRP B 279 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9636) covalent geometry : angle 0.52534 / 0.27 (13020) hydrogen bonds : bond 0.04325 / 2.91 ( 634) hydrogen bonds : angle 3.64477 / 2.70 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.381 Fit side-chains REVERT: A 572 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8316 (tpt) REVERT: A 666 LEU cc_start: 0.6987 (tm) cc_final: 0.6777 (tm) REVERT: B 666 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6777 (tm) outliers start: 24 outliers final: 7 residues processed: 125 average time/residue: 0.4279 time to fit residues: 58.3646 Evaluate side-chains 109 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108855 restraints weight = 11044.380| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.12 r_work: 0.3214 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9636 Z= 0.178 Angle : 0.532 6.627 13020 Z= 0.271 Chirality : 0.042 0.159 1496 Planarity : 0.003 0.024 1620 Dihedral : 8.916 125.366 1374 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.19 % Allowed : 14.67 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1166 helix: 1.47 (0.18), residues: 784 sheet: -1.81 (0.59), residues: 62 loop : -1.59 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.013 0.002 TYR A 667 PHE 0.019 0.001 PHE B 350 TRP 0.008 0.001 TRP B 463 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9636) covalent geometry : angle 0.53229 / 0.27 (13020) hydrogen bonds : bond 0.04531 / 3.07 ( 634) hydrogen bonds : angle 3.68987 / 2.74 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.221 Fit side-chains REVERT: A 134 GLN cc_start: 0.6848 (mt0) cc_final: 0.6613 (mt0) REVERT: A 421 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8301 (m-40) REVERT: A 556 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7415 (mptt) REVERT: A 572 MET cc_start: 0.8557 (mmm) cc_final: 0.8203 (tpt) REVERT: A 581 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7325 (mp) REVERT: A 666 LEU cc_start: 0.6934 (tm) cc_final: 0.6729 (tm) REVERT: B 134 GLN cc_start: 0.6945 (mt0) cc_final: 0.6713 (mt0) REVERT: B 421 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8325 (m-40) REVERT: B 556 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7423 (mptt) REVERT: B 581 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7310 (mp) REVERT: B 666 LEU cc_start: 0.6984 (tm) cc_final: 0.6778 (tm) outliers start: 32 outliers final: 6 residues processed: 132 average time/residue: 0.4817 time to fit residues: 69.0742 Evaluate side-chains 118 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111312 restraints weight = 11026.811| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.13 r_work: 0.3241 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9636 Z= 0.124 Angle : 0.491 7.093 13020 Z= 0.251 Chirality : 0.040 0.159 1496 Planarity : 0.003 0.024 1620 Dihedral : 8.657 125.167 1374 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 15.47 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1166 helix: 1.77 (0.18), residues: 786 sheet: -2.22 (0.58), residues: 52 loop : -1.37 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.022 0.001 TYR B 161 PHE 0.015 0.001 PHE B 350 TRP 0.008 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9636) covalent geometry : angle 0.49090 / 0.25 (13020) hydrogen bonds : bond 0.04118 / 2.77 ( 634) hydrogen bonds : angle 3.49664 / 2.59 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.343 Fit side-chains REVERT: A 134 GLN cc_start: 0.6743 (mt0) cc_final: 0.6498 (mt0) REVERT: A 556 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7370 (mptt) REVERT: B 134 GLN cc_start: 0.6738 (mt0) cc_final: 0.6510 (mt0) REVERT: B 350 PHE cc_start: 0.7263 (t80) cc_final: 0.6601 (t80) REVERT: B 556 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7383 (mptt) REVERT: B 662 MET cc_start: 0.6670 (tmm) cc_final: 0.6450 (ttt) outliers start: 26 outliers final: 8 residues processed: 135 average time/residue: 0.4577 time to fit residues: 67.1049 Evaluate side-chains 121 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111061 restraints weight = 10946.459| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.16 r_work: 0.3242 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9636 Z= 0.128 Angle : 0.495 7.573 13020 Z= 0.253 Chirality : 0.040 0.168 1496 Planarity : 0.003 0.025 1620 Dihedral : 8.504 124.523 1374 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.10 % Allowed : 16.37 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1166 helix: 1.86 (0.18), residues: 786 sheet: -2.14 (0.58), residues: 52 loop : -1.28 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 97 TYR 0.029 0.001 TYR B 161 PHE 0.024 0.001 PHE A 254 TRP 0.007 0.001 TRP A 279 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9636) covalent geometry : angle 0.49470 / 0.25 (13020) hydrogen bonds : bond 0.04135 / 2.78 ( 634) hydrogen bonds : angle 3.50294 / 2.60 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.385 Fit side-chains REVERT: A 134 GLN cc_start: 0.6700 (mt0) cc_final: 0.6451 (mt0) REVERT: A 350 PHE cc_start: 0.7040 (t80) cc_final: 0.6464 (t80) REVERT: A 556 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7368 (mptt) REVERT: A 572 MET cc_start: 0.8398 (mmm) cc_final: 0.8007 (tpt) REVERT: A 581 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 134 GLN cc_start: 0.6738 (mt0) cc_final: 0.6509 (mt0) REVERT: B 350 PHE cc_start: 0.7245 (t80) cc_final: 0.6617 (t80) REVERT: B 556 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7383 (mptt) REVERT: B 581 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7194 (mp) outliers start: 21 outliers final: 7 residues processed: 131 average time/residue: 0.4919 time to fit residues: 70.0088 Evaluate side-chains 122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 379 ASN B 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110282 restraints weight = 10950.843| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.17 r_work: 0.3239 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9636 Z= 0.143 Angle : 0.512 7.706 13020 Z= 0.260 Chirality : 0.040 0.163 1496 Planarity : 0.003 0.028 1620 Dihedral : 8.460 124.650 1374 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.10 % Allowed : 17.47 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1166 helix: 1.90 (0.18), residues: 782 sheet: -2.16 (0.58), residues: 52 loop : -1.24 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 97 TYR 0.032 0.001 TYR B 161 PHE 0.022 0.001 PHE A 254 TRP 0.008 0.001 TRP B 463 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9636) covalent geometry : angle 0.51151 / 0.26 (13020) hydrogen bonds : bond 0.04250 / 2.87 ( 634) hydrogen bonds : angle 3.53917 / 2.63 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.276 Fit side-chains REVERT: A 350 PHE cc_start: 0.7283 (t80) cc_final: 0.6704 (t80) REVERT: A 556 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7466 (mptt) REVERT: A 581 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7408 (mp) REVERT: B 134 GLN cc_start: 0.6906 (mt0) cc_final: 0.6684 (mt0) REVERT: B 350 PHE cc_start: 0.7404 (t80) cc_final: 0.6767 (t80) REVERT: B 556 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7482 (mptt) REVERT: B 581 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7404 (mp) outliers start: 21 outliers final: 6 residues processed: 126 average time/residue: 0.4390 time to fit residues: 60.0199 Evaluate side-chains 118 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112196 restraints weight = 10918.816| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.17 r_work: 0.3201 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9636 Z= 0.122 Angle : 0.497 8.113 13020 Z= 0.252 Chirality : 0.040 0.161 1496 Planarity : 0.003 0.028 1620 Dihedral : 8.297 124.411 1374 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.50 % Allowed : 18.56 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1166 helix: 2.02 (0.18), residues: 782 sheet: -2.16 (0.58), residues: 52 loop : -1.17 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.030 0.001 TYR B 161 PHE 0.020 0.001 PHE A 254 TRP 0.008 0.001 TRP A 279 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9636) covalent geometry : angle 0.49728 / 0.25 (13020) hydrogen bonds : bond 0.04055 / 2.73 ( 634) hydrogen bonds : angle 3.46513 / 2.57 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.285 Fit side-chains REVERT: A 350 PHE cc_start: 0.7180 (t80) cc_final: 0.6670 (t80) REVERT: A 556 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7480 (mptt) REVERT: A 581 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7405 (mp) REVERT: B 350 PHE cc_start: 0.7476 (t80) cc_final: 0.6759 (t80) REVERT: B 556 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7501 (mptt) REVERT: B 572 MET cc_start: 0.8535 (mmm) cc_final: 0.8164 (tpt) REVERT: B 581 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7402 (mp) outliers start: 15 outliers final: 4 residues processed: 125 average time/residue: 0.3876 time to fit residues: 53.0248 Evaluate side-chains 116 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111661 restraints weight = 10804.283| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.13 r_work: 0.3252 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9636 Z= 0.134 Angle : 0.512 7.913 13020 Z= 0.260 Chirality : 0.040 0.172 1496 Planarity : 0.003 0.028 1620 Dihedral : 8.181 124.172 1374 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.80 % Allowed : 18.56 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1166 helix: 2.02 (0.18), residues: 782 sheet: -2.05 (0.59), residues: 52 loop : -1.13 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.028 0.001 TYR B 161 PHE 0.020 0.001 PHE A 254 TRP 0.009 0.001 TRP A 463 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9636) covalent geometry : angle 0.51249 / 0.26 (13020) hydrogen bonds : bond 0.04141 / 2.79 ( 634) hydrogen bonds : angle 3.49849 / 2.60 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.352 Fit side-chains REVERT: A 350 PHE cc_start: 0.7128 (t80) cc_final: 0.6586 (t80) REVERT: A 556 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7417 (mptt) REVERT: A 581 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 350 PHE cc_start: 0.7358 (t80) cc_final: 0.6627 (t80) REVERT: B 556 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7436 (mptt) REVERT: B 572 MET cc_start: 0.8483 (mmm) cc_final: 0.8174 (tpt) REVERT: B 581 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7293 (mp) outliers start: 18 outliers final: 8 residues processed: 120 average time/residue: 0.4195 time to fit residues: 54.7912 Evaluate side-chains 122 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113913 restraints weight = 10765.353| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.11 r_work: 0.3266 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9636 Z= 0.115 Angle : 0.496 8.049 13020 Z= 0.251 Chirality : 0.039 0.173 1496 Planarity : 0.003 0.029 1620 Dihedral : 7.924 123.112 1374 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.40 % Allowed : 19.36 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.25), residues: 1166 helix: 2.18 (0.18), residues: 782 sheet: -2.02 (0.60), residues: 52 loop : -1.05 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.027 0.001 TYR B 161 PHE 0.018 0.001 PHE A 254 TRP 0.009 0.001 TRP B 279 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9636) covalent geometry : angle 0.49612 / 0.25 (13020) hydrogen bonds : bond 0.03916 / 2.63 ( 634) hydrogen bonds : angle 3.40645 / 2.53 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.69 seconds wall clock time: 47 minutes 57.44 seconds (2877.44 seconds total)