Starting phenix.real_space_refine on Sat Oct 24 19:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m4e_63624/10_2026/9m4e_63624.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9057 2.51 5 N 2475 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4773 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain: "B" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4773 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain: "C" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4773 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 588} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14319 At special positions: 0 Unit cell: (107.226, 110.63, 161.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2739 8.00 N 2475 7.00 C 9057 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: 0.91 Conformation dependent library (CDL) restraints added in 675.9 milliseconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 13.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.600A pdb=" N MET A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 361 through 364 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.686A pdb=" N LEU A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.976A pdb=" N ARG A 500 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 361 through 364 Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.500A pdb=" N MET B 445 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.695A pdb=" N LEU B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 486 " --> pdb=" O HIS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.968A pdb=" N ARG B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 250 through 265 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 441 through 445 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.713A pdb=" N LEU C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 removed outlier: 3.971A pdb=" N ARG C 500 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 270 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 268 through 270 current: chain 'A' and resid 313 through 320 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 636 removed outlier: 6.922A pdb=" N GLN B 639 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ARG C 657 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 641 " --> pdb=" O ARG C 657 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TRP C 659 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER B 643 " --> pdb=" O TRP C 659 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE C 672 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA C 655 " --> pdb=" O TYR C 670 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR C 670 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG C 657 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 668 " --> pdb=" O ARG C 657 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP C 659 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 666 " --> pdb=" O TRP C 659 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 632 through 636 removed outlier: 6.764A pdb=" N ILE A 640 " --> pdb=" O ALA C 634 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY C 636 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU A 642 " --> pdb=" O GLY C 636 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 639 " --> pdb=" O ALA B 655 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ARG B 657 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 641 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TRP B 659 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 643 " --> pdb=" O TRP B 659 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE B 672 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA B 655 " --> pdb=" O TYR B 670 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 670 " --> pdb=" O ALA B 655 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 657 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR B 668 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP B 659 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN B 666 " --> pdb=" O TRP B 659 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 677 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 632 through 636 removed outlier: 7.057A pdb=" N PHE A 672 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA A 655 " --> pdb=" O TYR A 670 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 670 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 657 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR A 668 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP A 659 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN A 666 " --> pdb=" O TRP A 659 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 677 " --> pdb=" O ARG B 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 693 through 698 removed outlier: 3.564A pdb=" N LYS A 713 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A 735 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 806 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 737 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 804 " --> pdb=" O THR A 737 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 708 removed outlier: 7.251A pdb=" N LEU A 744 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 789 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 746 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 270 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 268 through 270 current: chain 'B' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 313 through 320 current: chain 'B' and resid 393 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 693 through 698 removed outlier: 3.581A pdb=" N LYS B 713 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER B 735 " --> pdb=" O ASN B 806 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B 806 " --> pdb=" O SER B 735 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 737 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 804 " --> pdb=" O THR B 737 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 707 through 708 removed outlier: 7.255A pdb=" N LEU B 744 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 789 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 746 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'C' and resid 268 through 270 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 268 through 270 current: chain 'C' and resid 313 through 320 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 320 current: chain 'C' and resid 393 through 412 Processing sheet with id=AB4, first strand: chain 'C' and resid 693 through 698 removed outlier: 3.571A pdb=" N LYS C 713 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER C 735 " --> pdb=" O ASN C 806 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 806 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 737 " --> pdb=" O THR C 804 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 804 " --> pdb=" O THR C 737 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 707 through 708 removed outlier: 7.219A pdb=" N LEU C 744 " --> pdb=" O LEU C 789 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C 789 " --> pdb=" O LEU C 744 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 746 " --> pdb=" O VAL C 787 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 660 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: 1.68 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4604 1.33 - 1.45: 2422 1.45 - 1.57: 7545 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 14652 Sorted by residual: bond pdb=" C TRP C 606 " pdb=" N GLY C 607 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.46e-02 4.69e+03 2.38e+00 bond pdb=" C GLY C 607 " pdb=" O GLY C 607 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.35e-02 5.49e+03 1.98e+00 bond pdb=" CA GLY C 607 " pdb=" C GLY C 607 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.29e+00 bond pdb=" N GLY C 607 " pdb=" CA GLY C 607 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.05e+00 bond pdb=" CG ARG C 319 " pdb=" CD ARG C 319 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.62e-01 ... (remaining 14647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 19325 1.36 - 2.72: 537 2.72 - 4.08: 89 4.08 - 5.44: 16 5.44 - 6.79: 7 Bond angle restraints: 19974 Sorted by residual: angle pdb=" C PRO C 446 " pdb=" N PRO C 447 " pdb=" CA PRO C 447 " ideal model delta sigma weight residual 119.84 114.33 5.51 1.25e+00 6.40e-01 1.94e+01 angle pdb=" C PRO B 446 " pdb=" N PRO B 447 " pdb=" CA PRO B 447 " ideal model delta sigma weight residual 119.84 114.38 5.46 1.25e+00 6.40e-01 1.91e+01 angle pdb=" C PRO A 446 " pdb=" N PRO A 447 " pdb=" CA PRO A 447 " ideal model delta sigma weight residual 119.84 114.41 5.43 1.25e+00 6.40e-01 1.89e+01 angle pdb=" C THR B 647 " pdb=" N ASN B 648 " pdb=" CA ASN B 648 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N THR B 646 " pdb=" CA THR B 646 " pdb=" C THR B 646 " ideal model delta sigma weight residual 114.04 110.27 3.77 1.24e+00 6.50e-01 9.26e+00 ... (remaining 19969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 7836 16.98 - 33.97: 545 33.97 - 50.95: 96 50.95 - 67.93: 19 67.93 - 84.91: 18 Dihedral angle restraints: 8514 sinusoidal: 3279 harmonic: 5235 Sorted by residual: dihedral pdb=" CA VAL C 605 " pdb=" C VAL C 605 " pdb=" N TRP C 606 " pdb=" CA TRP C 606 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA VAL B 605 " pdb=" C VAL B 605 " pdb=" N TRP B 606 " pdb=" CA TRP B 606 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 605 " pdb=" C VAL A 605 " pdb=" N TRP A 606 " pdb=" CA TRP A 606 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 8511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1299 0.033 - 0.065: 550 0.065 - 0.098: 187 0.098 - 0.131: 156 0.131 - 0.163: 19 Chirality restraints: 2211 Sorted by residual: chirality pdb=" CA VAL B 765 " pdb=" N VAL B 765 " pdb=" C VAL B 765 " pdb=" CB VAL B 765 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ASN B 648 " pdb=" N ASN B 648 " pdb=" C ASN B 648 " pdb=" CB ASN B 648 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA VAL C 765 " pdb=" N VAL C 765 " pdb=" C VAL C 765 " pdb=" CB VAL C 765 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 2208 not shown) Planarity restraints: 2559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 446 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO C 447 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 447 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 447 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 446 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 447 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 446 " 0.038 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 447 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " 0.033 5.00e-02 4.00e+02 ... (remaining 2556 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 506 2.72 - 3.26: 13108 3.26 - 3.81: 22825 3.81 - 4.35: 30163 4.35 - 4.90: 51553 Nonbonded interactions: 118155 Sorted by model distance: nonbonded pdb=" OH TYR C 356 " pdb=" OE1 GLU C 358 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLU A 358 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR B 356 " pdb=" OE1 GLU B 358 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG A 790 " pdb=" O PRO A 795 " model vdw 2.276 3.120 nonbonded pdb=" NH1 ARG B 790 " pdb=" O PRO B 795 " model vdw 2.280 3.120 ... (remaining 118150 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 11.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 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 : 0.005 0.040 14652 Z= 0.193 Angle : 0.567 6.794 19974 Z= 0.317 Chirality : 0.048 0.163 2211 Planarity : 0.005 0.057 2559 Dihedral : 12.841 84.913 5238 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.84 (0.19), residues: 1833 helix: -1.27 (0.38), residues: 180 sheet: 0.08 (0.22), residues: 588 loop : -0.76 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 652 TYR 0.017 0.001 TYR A 356 PHE 0.006 0.001 PHE A 253 TRP 0.011 0.001 TRP B 454 HIS 0.003 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (14652) covalent geometry : angle 0.56707 / 0.32 (19974) hydrogen bonds : bond 0.17957 / 11.23 ( 275) hydrogen bonds : angle 6.88166 / 4.80 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4763 time to fit residues: 71.1918 Evaluate side-chains 113 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN C 332 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.064920 restraints weight = 22029.584| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.97 r_work: 0.2663 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9347 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14652 Z= 0.100 Angle : 0.468 6.055 19974 Z= 0.256 Chirality : 0.046 0.155 2211 Planarity : 0.004 0.054 2559 Dihedral : 4.419 19.467 2076 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.18 % Allowed : 5.19 % Favored : 93.62 % 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: -0.61 (0.20), residues: 1833 helix: -0.37 (0.37), residues: 198 sheet: 0.17 (0.23), residues: 591 loop : -0.72 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.011 0.001 TYR C 356 PHE 0.004 0.001 PHE A 253 TRP 0.012 0.001 TRP C 454 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14652) covalent geometry : angle 0.46816 / 0.26 (19974) hydrogen bonds : bond 0.03432 / 2.28 ( 275) hydrogen bonds : angle 5.04782 / 3.52 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.411 Fit side-chains REVERT: A 240 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8361 (mmtm) REVERT: C 238 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: C 712 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8192 (tm-30) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.4922 time to fit residues: 72.6258 Evaluate side-chains 126 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 596 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [64, 59, 15, 119, 139, 23, 151, 145, 93, 11, 133] chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.064114 restraints weight = 22499.689| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.99 r_work: 0.2635 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9362 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14652 Z= 0.139 Angle : 0.487 5.794 19974 Z= 0.268 Chirality : 0.047 0.155 2211 Planarity : 0.004 0.055 2559 Dihedral : 4.455 20.059 2076 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.25 % Allowed : 7.03 % Favored : 91.72 % 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 (0.20), residues: 1833 helix: -0.14 (0.38), residues: 201 sheet: 0.29 (0.22), residues: 612 loop : -0.76 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.012 0.001 TYR A 448 PHE 0.005 0.001 PHE A 253 TRP 0.010 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14652) covalent geometry : angle 0.48738 / 0.27 (19974) hydrogen bonds : bond 0.03704 / 2.45 ( 275) hydrogen bonds : angle 4.88491 / 3.43 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.592 Fit side-chains REVERT: A 240 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8283 (mmtm) REVERT: C 450 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: C 712 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8210 (tm-30) outliers start: 19 outliers final: 12 residues processed: 128 average time/residue: 0.4753 time to fit residues: 68.2887 Evaluate side-chains 131 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 774 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [107, 9, 71, 54, 70, 105, 126, 68, 60, 36, 121] chunk 107 optimal weight: 0.0370 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.064843 restraints weight = 22254.883| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.97 r_work: 0.2662 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9344 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14652 Z= 0.097 Angle : 0.446 5.709 19974 Z= 0.245 Chirality : 0.046 0.148 2211 Planarity : 0.004 0.055 2559 Dihedral : 4.217 19.884 2076 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.05 % Allowed : 8.55 % Favored : 90.40 % 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: -0.39 (0.20), residues: 1833 helix: 0.12 (0.39), residues: 198 sheet: 0.30 (0.23), residues: 585 loop : -0.62 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.012 0.001 TYR C 448 PHE 0.005 0.001 PHE B 253 TRP 0.010 0.001 TRP B 599 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14652) covalent geometry : angle 0.44599 / 0.24 (19974) hydrogen bonds : bond 0.03065 / 2.04 ( 275) hydrogen bonds : angle 4.68804 / 3.30 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.360 Fit side-chains REVERT: A 240 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8301 (mmtm) REVERT: B 212 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8494 (mmp) REVERT: C 450 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: C 712 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8228 (tm-30) outliers start: 16 outliers final: 7 residues processed: 136 average time/residue: 0.4387 time to fit residues: 67.1833 Evaluate side-chains 126 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 774 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [169, 21, 124, 164, 181, 43, 113, 35, 99, 2, 102] chunk 169 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 GLN A 741 ASN B 332 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.062478 restraints weight = 22471.611| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.97 r_work: 0.2593 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9387 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14652 Z= 0.269 Angle : 0.579 5.640 19974 Z= 0.320 Chirality : 0.051 0.167 2211 Planarity : 0.005 0.056 2559 Dihedral : 4.828 24.255 2076 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.71 % Allowed : 8.81 % Favored : 89.48 % 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: -0.56 (0.20), residues: 1833 helix: 0.12 (0.40), residues: 183 sheet: 0.21 (0.22), residues: 606 loop : -0.79 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 319 TYR 0.013 0.002 TYR B 684 PHE 0.008 0.001 PHE A 253 TRP 0.012 0.002 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.27 (14652) covalent geometry : angle 0.57871 / 0.32 (19974) hydrogen bonds : bond 0.04496 / 2.99 ( 275) hydrogen bonds : angle 4.99318 / 3.51 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.485 Fit side-chains REVERT: A 240 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (mmtm) REVERT: A 511 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8617 (mt0) REVERT: B 238 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: B 240 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8549 (mmtm) REVERT: B 450 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: C 450 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8304 (m-30) outliers start: 26 outliers final: 10 residues processed: 135 average time/residue: 0.4999 time to fit residues: 75.6512 Evaluate side-chains 132 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [78, 72, 138, 168, 137, 0, 159, 151, 106, 112, 116] chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** C 511 GLN ** 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 = 0.3166 r_free = 0.3166 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.064281 restraints weight = 22263.392| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.97 r_work: 0.2632 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9364 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14652 Z= 0.129 Angle : 0.483 5.704 19974 Z= 0.267 Chirality : 0.047 0.155 2211 Planarity : 0.004 0.054 2559 Dihedral : 4.502 20.602 2076 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.51 % Allowed : 9.14 % Favored : 89.35 % 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: -0.56 (0.20), residues: 1833 helix: -0.09 (0.38), residues: 201 sheet: 0.22 (0.23), residues: 579 loop : -0.74 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 307 TYR 0.012 0.001 TYR B 448 PHE 0.005 0.001 PHE A 253 TRP 0.010 0.001 TRP C 454 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (14652) covalent geometry : angle 0.48300 / 0.27 (19974) hydrogen bonds : bond 0.03392 / 2.26 ( 275) hydrogen bonds : angle 4.75460 / 3.33 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.583 Fit side-chains REVERT: A 240 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8312 (mmtm) REVERT: A 276 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: A 511 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8752 (mt0) REVERT: B 238 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: B 240 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8516 (mmtm) REVERT: C 450 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8276 (m-30) outliers start: 23 outliers final: 10 residues processed: 134 average time/residue: 0.4828 time to fit residues: 72.8659 Evaluate side-chains 135 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [88, 139, 132, 107, 8, 61, 148, 102, 52, 114, 45] chunk 88 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.087341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.063579 restraints weight = 22100.403| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.96 r_work: 0.2636 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14652 Z= 0.130 Angle : 0.483 5.605 19974 Z= 0.266 Chirality : 0.047 0.152 2211 Planarity : 0.004 0.054 2559 Dihedral : 4.432 19.492 2076 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.45 % Allowed : 9.53 % Favored : 89.02 % 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: -0.48 (0.20), residues: 1833 helix: -0.04 (0.39), residues: 201 sheet: 0.26 (0.22), residues: 612 loop : -0.70 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 307 TYR 0.012 0.001 TYR B 448 PHE 0.005 0.001 PHE A 253 TRP 0.009 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14652) covalent geometry : angle 0.48285 / 0.27 (19974) hydrogen bonds : bond 0.03373 / 2.24 ( 275) hydrogen bonds : angle 4.69586 / 3.29 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.488 Fit side-chains REVERT: A 240 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8308 (mmtm) REVERT: A 276 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: B 238 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: B 240 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8518 (mmtm) REVERT: C 450 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8261 (m-30) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 0.4839 time to fit residues: 71.8532 Evaluate side-chains 136 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [174, 27, 144, 89, 5, 3, 115, 51, 52, 152, 13] chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.087555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.063866 restraints weight = 22306.125| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.97 r_work: 0.2626 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9369 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14652 Z= 0.151 Angle : 0.499 5.582 19974 Z= 0.275 Chirality : 0.047 0.153 2211 Planarity : 0.004 0.055 2559 Dihedral : 4.504 20.348 2076 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.45 % Allowed : 9.66 % Favored : 88.89 % 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: -0.51 (0.20), residues: 1833 helix: -0.08 (0.39), residues: 201 sheet: 0.25 (0.22), residues: 606 loop : -0.73 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 307 TYR 0.012 0.001 TYR B 448 PHE 0.006 0.001 PHE A 253 TRP 0.011 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (14652) covalent geometry : angle 0.49865 / 0.28 (19974) hydrogen bonds : bond 0.03583 / 2.38 ( 275) hydrogen bonds : angle 4.72568 / 3.31 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.673 Fit side-chains REVERT: A 240 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (mmtm) REVERT: A 276 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: B 240 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8533 (mmtm) REVERT: C 450 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8264 (m-30) outliers start: 22 outliers final: 12 residues processed: 136 average time/residue: 0.5004 time to fit residues: 76.3663 Evaluate side-chains 135 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [80, 157, 131, 124, 173, 86, 137, 148, 121, 73, 64] chunk 80 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.085433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061891 restraints weight = 22588.079| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.97 r_work: 0.2584 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9394 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14652 Z= 0.305 Angle : 0.610 6.266 19974 Z= 0.338 Chirality : 0.052 0.179 2211 Planarity : 0.005 0.056 2559 Dihedral : 4.949 25.015 2076 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.51 % Allowed : 9.99 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1833 helix: 0.04 (0.40), residues: 183 sheet: 0.13 (0.22), residues: 606 loop : -0.86 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 307 TYR 0.013 0.002 TYR B 448 PHE 0.008 0.001 PHE A 399 TRP 0.012 0.002 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.31 (14652) covalent geometry : angle 0.61050 / 0.34 (19974) hydrogen bonds : bond 0.04674 / 3.10 ( 275) hydrogen bonds : angle 5.03823 / 3.54 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.445 Fit side-chains REVERT: A 238 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8710 (m-30) REVERT: A 240 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (mmtm) REVERT: A 276 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: B 240 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8571 (mmtm) REVERT: C 450 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8348 (m-30) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.5036 time to fit residues: 74.4363 Evaluate side-chains 131 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [17, 71, 43, 103, 122, 114, 52, 178, 120, 181, 63] chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062775 restraints weight = 22367.362| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.97 r_work: 0.2602 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9384 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14652 Z= 0.217 Angle : 0.555 6.436 19974 Z= 0.307 Chirality : 0.049 0.174 2211 Planarity : 0.005 0.055 2559 Dihedral : 4.829 23.804 2076 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.25 % Allowed : 10.45 % Favored : 88.30 % 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: -0.64 (0.20), residues: 1833 helix: 0.12 (0.40), residues: 183 sheet: 0.13 (0.22), residues: 606 loop : -0.84 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 307 TYR 0.012 0.001 TYR B 448 PHE 0.007 0.001 PHE A 253 TRP 0.011 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (14652) covalent geometry : angle 0.55477 / 0.31 (19974) hydrogen bonds : bond 0.04100 / 2.72 ( 275) hydrogen bonds : angle 4.93909 / 3.46 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.489 Fit side-chains REVERT: A 238 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (m-30) REVERT: A 240 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8386 (mmtm) REVERT: A 276 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 511 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: B 240 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8543 (mmtm) REVERT: C 450 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8294 (m-30) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 0.5002 time to fit residues: 72.9579 Evaluate side-chains 135 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: [141, 168, 174, 97, 155, 88, 20, 28, 169, 111, 108] chunk 141 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.061987 restraints weight = 22282.086| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.97 r_work: 0.2606 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9384 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 14652 Z= 0.213 Angle : 0.786 59.169 19974 Z= 0.460 Chirality : 0.049 0.235 2211 Planarity : 0.005 0.055 2559 Dihedral : 4.828 23.841 2076 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.25 % Allowed : 10.32 % Favored : 88.43 % Cbeta Deviations : 0.06 % 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: -0.64 (0.20), residues: 1833 helix: 0.13 (0.40), residues: 183 sheet: 0.13 (0.22), residues: 606 loop : -0.84 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 307 TYR 0.012 0.001 TYR B 448 PHE 0.006 0.001 PHE A 253 TRP 0.011 0.001 TRP C 454 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (14652) covalent geometry : angle 0.78642 / 0.46 (19974) hydrogen bonds : bond 0.04037 / 2.68 ( 275) hydrogen bonds : angle 4.93733 / 3.46 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.65 seconds wall clock time: 77 minutes 39.45 seconds (4659.45 seconds total)