Starting phenix.real_space_refine on Wed Feb 4 01:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.map" model { file = "/net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baw_44412/02_2026/9baw_44412.cif" } resolution = 3.3 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= 0.018 sd= 0.039 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 3 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 5194 2.51 5 N 1393 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8223 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6810 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 838} Chain: "B" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1380 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.02, per 1000 atoms: 0.25 Number of scatterers: 8223 At special positions: 0 Unit cell: (84.293, 92.829, 112.035, 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 51 16.00 P 3 15.00 Mg 1 11.99 O 1581 8.00 N 1393 7.00 C 5194 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 Atom "HETATM 8214 O3A GTP B 201 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8215 O3B GTP B 201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 310.2 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 1 sheets defined 75.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.634A pdb=" N ILE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.769A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.971A pdb=" N CYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.668A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.541A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.813A pdb=" N LYS A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 230 through 248 Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.600A pdb=" N MET A 252 " --> pdb=" O TYR A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.792A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 318 through 330 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 363 through 375 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.627A pdb=" N ARG A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 Proline residue: A 404 - end of helix Proline residue: A 411 - end of helix removed outlier: 3.723A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.070A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.983A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 4.026A pdb=" N SER A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 543 through 563 Processing helix chain 'A' and resid 570 through 593 removed outlier: 5.466A pdb=" N GLN A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 618 removed outlier: 3.959A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 640 removed outlier: 3.570A pdb=" N MET A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.045A pdb=" N LEU A 644 " --> pdb=" O GLY A 641 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 645' Processing helix chain 'A' and resid 646 through 661 Proline residue: A 652 - end of helix removed outlier: 4.256A pdb=" N TYR A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 Processing helix chain 'A' and resid 685 through 699 removed outlier: 3.848A pdb=" N ASP A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 4.008A pdb=" N GLN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.844A pdb=" N LYS A 729 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 730 " --> pdb=" O GLU A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 730' Processing helix chain 'A' and resid 731 through 745 removed outlier: 3.543A pdb=" N ALA A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 777 removed outlier: 4.072A pdb=" N ASP A 756 " --> pdb=" O TYR A 752 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 790 Processing helix chain 'A' and resid 792 through 807 removed outlier: 4.336A pdb=" N PHE A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.721A pdb=" N VAL A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 removed outlier: 3.645A pdb=" N LEU A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 853 removed outlier: 4.393A pdb=" N HIS A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.930A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 75 through 81 removed outlier: 4.078A pdb=" N ILE B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.869A pdb=" N TYR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.558A pdb=" N LYS B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 54 removed outlier: 3.683A pdb=" N THR B 54 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE B 11 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TRP B 64 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 13 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR B 66 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 15 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS B 12 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE B 87 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 14 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N MET B 89 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 16 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 86 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N CYS B 120 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 88 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 122 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B 90 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 145 " --> pdb=" O ILE B 117 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1554 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: 1.16 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2730 1.34 - 1.46: 1426 1.46 - 1.58: 4133 1.58 - 1.69: 5 1.69 - 1.81: 76 Bond restraints: 8370 Sorted by residual: bond pdb=" C ARG A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.333 1.365 -0.032 1.20e-02 6.94e+03 7.18e+00 bond pdb=" C LYS B 159 " pdb=" N PRO B 160 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C VAL A 323 " pdb=" N PRO A 324 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.63e+00 bond pdb=" N ASN A 702 " pdb=" CA ASN A 702 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.56e+00 bond pdb=" C ILE A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.49e+00 ... (remaining 8365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11212 2.13 - 4.27: 115 4.27 - 6.40: 22 6.40 - 8.53: 11 8.53 - 10.67: 2 Bond angle restraints: 11362 Sorted by residual: angle pdb=" C ILE A 363 " pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 120.33 123.04 -2.71 8.00e-01 1.56e+00 1.15e+01 angle pdb=" N VAL A 790 " pdb=" CA VAL A 790 " pdb=" C VAL A 790 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 angle pdb=" CD LYS B 123 " pdb=" CE LYS B 123 " pdb=" NZ LYS B 123 " ideal model delta sigma weight residual 111.90 101.23 10.67 3.20e+00 9.77e-02 1.11e+01 angle pdb=" C ASN A 522 " pdb=" N ASN A 523 " pdb=" CA ASN A 523 " ideal model delta sigma weight residual 122.46 126.60 -4.14 1.41e+00 5.03e-01 8.61e+00 angle pdb=" C VAL A 624 " pdb=" N GLN A 625 " pdb=" CA GLN A 625 " ideal model delta sigma weight residual 122.08 126.19 -4.11 1.47e+00 4.63e-01 7.81e+00 ... (remaining 11357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 5000 31.38 - 62.77: 108 62.77 - 94.15: 4 94.15 - 125.54: 1 125.54 - 156.92: 2 Dihedral angle restraints: 5115 sinusoidal: 2051 harmonic: 3064 Sorted by residual: dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual 291.08 134.16 156.92 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -39.86 144.45 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O5' GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PA GTP B 201 " pdb=" PB GTP B 201 " ideal model delta sinusoidal sigma weight residual 274.12 165.98 108.15 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 5112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 858 0.034 - 0.069: 309 0.069 - 0.103: 105 0.103 - 0.137: 33 0.137 - 0.171: 3 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CA TYR A 661 " pdb=" N TYR A 661 " pdb=" C TYR A 661 " pdb=" CB TYR A 661 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA LYS B 159 " pdb=" N LYS B 159 " pdb=" C LYS B 159 " pdb=" CB LYS B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CB ILE A 685 " pdb=" CA ILE A 685 " pdb=" CG1 ILE A 685 " pdb=" CG2 ILE A 685 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1305 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO A 397 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 343 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO A 344 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GTP B 201 " -0.006 2.00e-02 2.50e+03 1.31e-02 5.12e+00 pdb=" C2 GTP B 201 " -0.004 2.00e-02 2.50e+03 pdb=" C4 GTP B 201 " 0.042 2.00e-02 2.50e+03 pdb=" C5 GTP B 201 " -0.009 2.00e-02 2.50e+03 pdb=" C6 GTP B 201 " -0.000 2.00e-02 2.50e+03 pdb=" C8 GTP B 201 " -0.006 2.00e-02 2.50e+03 pdb=" N1 GTP B 201 " -0.001 2.00e-02 2.50e+03 pdb=" N2 GTP B 201 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP B 201 " -0.011 2.00e-02 2.50e+03 pdb=" N7 GTP B 201 " 0.000 2.00e-02 2.50e+03 pdb=" N9 GTP B 201 " -0.004 2.00e-02 2.50e+03 pdb=" O6 GTP B 201 " 0.000 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 82 2.58 - 3.16: 6677 3.16 - 3.74: 13600 3.74 - 4.32: 17493 4.32 - 4.90: 29401 Nonbonded interactions: 67253 Sorted by model distance: nonbonded pdb=" O3G GTP B 201 " pdb="MG MG B 202 " model vdw 2.005 2.170 nonbonded pdb=" O2B GTP B 201 " pdb="MG MG B 202 " model vdw 2.037 2.170 nonbonded pdb=" N GLY B 20 " pdb=" O3B GTP B 201 " model vdw 2.188 2.496 nonbonded pdb=" NZ LYS B 123 " pdb=" N3 GTP B 201 " model vdw 2.243 2.560 nonbonded pdb=" O LEU A 7 " pdb=" OG1 THR A 10 " model vdw 2.268 3.040 ... (remaining 67248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.800 Find NCS groups from input model: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.003 0.036 8372 Z= 0.145 Angle : 0.623 10.667 11362 Z= 0.327 Chirality : 0.042 0.171 1308 Planarity : 0.005 0.066 1471 Dihedral : 12.871 156.924 3125 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 4.12 % Allowed : 5.23 % Favored : 90.66 % 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: 0.55 (0.25), residues: 1042 helix: 0.87 (0.18), residues: 716 sheet: 0.25 (0.83), residues: 39 loop : -0.73 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.016 0.001 TYR A 661 PHE 0.018 0.001 PHE A 577 TRP 0.012 0.001 TRP A 430 HIS 0.002 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8370) covalent geometry : angle 0.62253 (11362) hydrogen bonds : bond 0.12516 ( 526) hydrogen bonds : angle 4.57474 ( 1554) Misc. bond : bond 0.00798 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 31 time to evaluate : 0.272 Fit side-chains REVERT: A 6 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 65 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8722 (tp) REVERT: A 146 MET cc_start: 0.8889 (tmm) cc_final: 0.8664 (tmm) REVERT: A 333 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: A 533 MET cc_start: 0.9086 (mtm) cc_final: 0.8755 (mtm) REVERT: A 665 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: A 693 MET cc_start: 0.8416 (tpp) cc_final: 0.8185 (tpp) outliers start: 37 outliers final: 10 residues processed: 65 average time/residue: 0.0689 time to fit residues: 6.8489 Evaluate side-chains 40 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 220 GLN A 227 GLN A 303 GLN A 616 GLN A 694 GLN B 10 GLN B 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.051501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037988 restraints weight = 53085.578| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.80 r_work: 0.3004 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8372 Z= 0.128 Angle : 0.560 9.790 11362 Z= 0.273 Chirality : 0.039 0.170 1308 Planarity : 0.004 0.059 1471 Dihedral : 9.913 161.077 1159 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.89 % Allowed : 7.12 % Favored : 90.99 % 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: 1.72 (0.27), residues: 1042 helix: 1.78 (0.19), residues: 728 sheet: -0.13 (0.76), residues: 39 loop : -0.32 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 27 TYR 0.016 0.001 TYR A 314 PHE 0.011 0.001 PHE A 577 TRP 0.010 0.001 TRP A 472 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8370) covalent geometry : angle 0.56015 (11362) hydrogen bonds : bond 0.03313 ( 526) hydrogen bonds : angle 3.66309 ( 1554) Misc. bond : bond 0.00469 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.273 Fit side-chains REVERT: A 65 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 333 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6880 (mp10) REVERT: A 388 MET cc_start: 0.8359 (tpt) cc_final: 0.7845 (tpt) REVERT: A 533 MET cc_start: 0.9365 (mtm) cc_final: 0.9054 (mtm) REVERT: A 647 MET cc_start: 0.9016 (tpt) cc_final: 0.8442 (tmm) REVERT: A 665 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: A 754 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8120 (mpp) outliers start: 17 outliers final: 8 residues processed: 42 average time/residue: 0.0548 time to fit residues: 3.7959 Evaluate side-chains 37 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.037924 restraints weight = 52857.768| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.75 r_work: 0.2998 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8372 Z= 0.132 Angle : 0.540 7.831 11362 Z= 0.261 Chirality : 0.039 0.139 1308 Planarity : 0.004 0.055 1471 Dihedral : 9.607 160.293 1152 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 1.89 % Allowed : 6.67 % Favored : 91.43 % 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: 2.09 (0.27), residues: 1042 helix: 2.12 (0.20), residues: 729 sheet: -0.25 (0.73), residues: 39 loop : -0.37 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.012 0.001 TYR A 661 PHE 0.011 0.001 PHE A 577 TRP 0.012 0.001 TRP A 472 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8370) covalent geometry : angle 0.53955 (11362) hydrogen bonds : bond 0.03120 ( 526) hydrogen bonds : angle 3.59087 ( 1554) Misc. bond : bond 0.00437 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8950 (tp) REVERT: A 146 MET cc_start: 0.9033 (tmm) cc_final: 0.8778 (tmm) REVERT: A 388 MET cc_start: 0.8384 (tpt) cc_final: 0.7999 (tpt) REVERT: A 533 MET cc_start: 0.9357 (mtm) cc_final: 0.9015 (mtm) REVERT: A 630 MET cc_start: 0.9436 (mtm) cc_final: 0.8915 (mtm) REVERT: A 647 MET cc_start: 0.8980 (tpt) cc_final: 0.8695 (tpt) REVERT: A 665 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: A 754 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (mpp) outliers start: 17 outliers final: 11 residues processed: 41 average time/residue: 0.0775 time to fit residues: 5.1457 Evaluate side-chains 39 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.051544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.038091 restraints weight = 53939.325| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.83 r_work: 0.2980 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8372 Z= 0.134 Angle : 0.536 8.086 11362 Z= 0.260 Chirality : 0.039 0.136 1308 Planarity : 0.004 0.055 1471 Dihedral : 9.397 160.284 1149 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.22 % Allowed : 6.79 % Favored : 90.99 % 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: 2.28 (0.27), residues: 1042 helix: 2.27 (0.20), residues: 731 sheet: -0.27 (0.75), residues: 39 loop : -0.31 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.018 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.009 0.001 TRP A 342 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8370) covalent geometry : angle 0.53644 (11362) hydrogen bonds : bond 0.03037 ( 526) hydrogen bonds : angle 3.56435 ( 1554) Misc. bond : bond 0.00428 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 146 MET cc_start: 0.9033 (tmm) cc_final: 0.8742 (tmm) REVERT: A 333 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 388 MET cc_start: 0.8399 (tpt) cc_final: 0.8058 (tpt) REVERT: A 533 MET cc_start: 0.9373 (mtm) cc_final: 0.9080 (mtm) REVERT: A 647 MET cc_start: 0.8958 (tpt) cc_final: 0.8635 (tpt) REVERT: A 665 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: A 754 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (mpp) outliers start: 20 outliers final: 13 residues processed: 44 average time/residue: 0.0754 time to fit residues: 5.3252 Evaluate side-chains 42 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.050798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.037190 restraints weight = 54626.907| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.82 r_work: 0.2957 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8372 Z= 0.177 Angle : 0.573 7.780 11362 Z= 0.279 Chirality : 0.040 0.141 1308 Planarity : 0.004 0.052 1471 Dihedral : 9.424 158.033 1149 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 2.45 % Allowed : 6.90 % Favored : 90.66 % 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: 2.36 (0.27), residues: 1042 helix: 2.32 (0.20), residues: 731 sheet: -0.36 (0.75), residues: 39 loop : -0.25 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.015 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.011 0.001 TRP A 283 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8370) covalent geometry : angle 0.57270 (11362) hydrogen bonds : bond 0.03198 ( 526) hydrogen bonds : angle 3.63501 ( 1554) Misc. bond : bond 0.00406 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 25 time to evaluate : 0.332 Fit side-chains REVERT: A 65 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 146 MET cc_start: 0.9062 (tmm) cc_final: 0.8730 (tmm) REVERT: A 333 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 388 MET cc_start: 0.8425 (tpt) cc_final: 0.8119 (tpt) REVERT: A 533 MET cc_start: 0.9402 (mtm) cc_final: 0.9134 (mtm) REVERT: A 630 MET cc_start: 0.9448 (mtm) cc_final: 0.8923 (mtm) REVERT: A 647 MET cc_start: 0.8962 (tpt) cc_final: 0.8629 (tpt) REVERT: A 665 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: A 754 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8074 (mpp) outliers start: 22 outliers final: 12 residues processed: 45 average time/residue: 0.0641 time to fit residues: 4.8019 Evaluate side-chains 41 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.037641 restraints weight = 53438.725| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.81 r_work: 0.2973 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8372 Z= 0.131 Angle : 0.540 8.010 11362 Z= 0.262 Chirality : 0.039 0.138 1308 Planarity : 0.004 0.053 1471 Dihedral : 9.413 159.877 1149 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.22 % Allowed : 7.56 % Favored : 90.21 % 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: 2.41 (0.27), residues: 1042 helix: 2.39 (0.20), residues: 731 sheet: -0.45 (0.76), residues: 39 loop : -0.29 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.025 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.010 0.001 TRP A 430 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8370) covalent geometry : angle 0.54025 (11362) hydrogen bonds : bond 0.03030 ( 526) hydrogen bonds : angle 3.58401 ( 1554) Misc. bond : bond 0.00429 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8993 (tp) REVERT: A 146 MET cc_start: 0.9043 (tmm) cc_final: 0.8717 (tmm) REVERT: A 333 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: A 388 MET cc_start: 0.8393 (tpt) cc_final: 0.8039 (tpt) REVERT: A 533 MET cc_start: 0.9379 (mtm) cc_final: 0.9101 (mtm) REVERT: A 564 MET cc_start: 0.7561 (ppp) cc_final: 0.7216 (ppp) REVERT: A 647 MET cc_start: 0.8949 (tpt) cc_final: 0.8620 (tpt) REVERT: A 665 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: A 754 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8044 (mpp) outliers start: 20 outliers final: 15 residues processed: 44 average time/residue: 0.0744 time to fit residues: 5.2608 Evaluate side-chains 44 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.051668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.038351 restraints weight = 53068.094| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.77 r_work: 0.3008 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8372 Z= 0.094 Angle : 0.516 8.027 11362 Z= 0.249 Chirality : 0.038 0.137 1308 Planarity : 0.004 0.056 1471 Dihedral : 9.353 163.502 1149 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.34 % Allowed : 7.68 % Favored : 89.99 % 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: 2.44 (0.27), residues: 1042 helix: 2.42 (0.20), residues: 735 sheet: -0.38 (0.77), residues: 39 loop : -0.38 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.015 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.033 0.001 TRP A 472 HIS 0.003 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8370) covalent geometry : angle 0.51580 (11362) hydrogen bonds : bond 0.02761 ( 526) hydrogen bonds : angle 3.48569 ( 1554) Misc. bond : bond 0.00475 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9001 (tp) REVERT: A 146 MET cc_start: 0.9026 (tmm) cc_final: 0.8693 (tmm) REVERT: A 333 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: A 388 MET cc_start: 0.8349 (tpt) cc_final: 0.7890 (tpt) REVERT: A 533 MET cc_start: 0.9355 (mtm) cc_final: 0.9047 (mtm) REVERT: A 564 MET cc_start: 0.7506 (ppp) cc_final: 0.7222 (ppp) REVERT: A 630 MET cc_start: 0.9314 (mtm) cc_final: 0.8648 (mpp) REVERT: A 647 MET cc_start: 0.8930 (tpt) cc_final: 0.8562 (tpt) REVERT: A 665 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: A 754 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8058 (mpp) outliers start: 21 outliers final: 14 residues processed: 46 average time/residue: 0.0696 time to fit residues: 5.0865 Evaluate side-chains 43 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.051887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.038509 restraints weight = 53336.520| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.80 r_work: 0.3014 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8372 Z= 0.097 Angle : 0.524 8.697 11362 Z= 0.253 Chirality : 0.038 0.137 1308 Planarity : 0.004 0.057 1471 Dihedral : 9.299 163.849 1149 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 2.22 % Allowed : 7.68 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.27), residues: 1042 helix: 2.42 (0.20), residues: 735 sheet: -0.25 (0.77), residues: 39 loop : -0.40 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.012 0.001 TYR A 661 PHE 0.012 0.001 PHE A 688 TRP 0.017 0.001 TRP A 472 HIS 0.002 0.000 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8370) covalent geometry : angle 0.52354 (11362) hydrogen bonds : bond 0.02831 ( 526) hydrogen bonds : angle 3.45693 ( 1554) Misc. bond : bond 0.00472 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9012 (tp) REVERT: A 146 MET cc_start: 0.8991 (tmm) cc_final: 0.8693 (tmm) REVERT: A 333 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: A 388 MET cc_start: 0.8372 (tpt) cc_final: 0.7914 (tpt) REVERT: A 533 MET cc_start: 0.9342 (mtm) cc_final: 0.9030 (mtm) REVERT: A 630 MET cc_start: 0.9287 (mtm) cc_final: 0.8616 (mpp) REVERT: A 647 MET cc_start: 0.8900 (tpt) cc_final: 0.8594 (tpt) REVERT: A 665 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: A 754 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8037 (mpp) outliers start: 20 outliers final: 14 residues processed: 45 average time/residue: 0.0724 time to fit residues: 5.2593 Evaluate side-chains 43 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 87 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.052226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.039010 restraints weight = 52907.981| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.78 r_work: 0.3038 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8372 Z= 0.091 Angle : 0.532 10.031 11362 Z= 0.255 Chirality : 0.038 0.152 1308 Planarity : 0.004 0.059 1471 Dihedral : 9.250 165.378 1149 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.89 % Allowed : 8.34 % Favored : 89.77 % 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: 2.42 (0.27), residues: 1042 helix: 2.40 (0.20), residues: 740 sheet: 0.05 (0.79), residues: 39 loop : -0.49 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.018 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.019 0.001 TRP A 472 HIS 0.004 0.000 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 8370) covalent geometry : angle 0.53179 (11362) hydrogen bonds : bond 0.02653 ( 526) hydrogen bonds : angle 3.40880 ( 1554) Misc. bond : bond 0.00497 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8948 (tp) REVERT: A 146 MET cc_start: 0.8949 (tmm) cc_final: 0.8677 (tmm) REVERT: A 219 MET cc_start: 0.8872 (mmm) cc_final: 0.8599 (mmm) REVERT: A 333 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: A 388 MET cc_start: 0.8339 (tpt) cc_final: 0.7825 (tpt) REVERT: A 533 MET cc_start: 0.9324 (mtm) cc_final: 0.8989 (mtm) REVERT: A 630 MET cc_start: 0.9238 (mtm) cc_final: 0.8608 (mpp) REVERT: A 647 MET cc_start: 0.8911 (tpt) cc_final: 0.8617 (tpt) REVERT: A 665 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: A 754 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8029 (mpp) outliers start: 17 outliers final: 13 residues processed: 42 average time/residue: 0.0787 time to fit residues: 5.2967 Evaluate side-chains 42 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.050776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037201 restraints weight = 54359.469| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.79 r_work: 0.2960 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8372 Z= 0.207 Angle : 0.615 9.657 11362 Z= 0.301 Chirality : 0.041 0.140 1308 Planarity : 0.004 0.051 1471 Dihedral : 9.311 157.373 1149 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.89 % Allowed : 8.45 % Favored : 89.66 % 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: 2.45 (0.27), residues: 1042 helix: 2.39 (0.20), residues: 735 sheet: -0.29 (0.79), residues: 39 loop : -0.26 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.026 0.001 TYR A 104 PHE 0.013 0.002 PHE A 688 TRP 0.040 0.002 TRP A 472 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8370) covalent geometry : angle 0.61458 (11362) hydrogen bonds : bond 0.03240 ( 526) hydrogen bonds : angle 3.64496 ( 1554) Misc. bond : bond 0.00377 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: A 388 MET cc_start: 0.8438 (tpt) cc_final: 0.8139 (tpt) REVERT: A 533 MET cc_start: 0.9415 (mtm) cc_final: 0.9154 (mtm) REVERT: A 630 MET cc_start: 0.9359 (mtm) cc_final: 0.8716 (mpp) REVERT: A 647 MET cc_start: 0.8973 (tpt) cc_final: 0.8630 (tpt) REVERT: A 665 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: A 754 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8057 (mpp) outliers start: 17 outliers final: 12 residues processed: 41 average time/residue: 0.0744 time to fit residues: 4.7811 Evaluate side-chains 40 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 664 TYR Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 123 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 97 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.051310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.037938 restraints weight = 53326.071| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.76 r_work: 0.2988 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8372 Z= 0.127 Angle : 0.561 9.698 11362 Z= 0.270 Chirality : 0.039 0.137 1308 Planarity : 0.004 0.053 1471 Dihedral : 9.261 160.124 1147 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.89 % Allowed : 8.68 % Favored : 89.43 % 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: 2.44 (0.27), residues: 1042 helix: 2.39 (0.20), residues: 741 sheet: -0.38 (0.78), residues: 39 loop : -0.31 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.019 0.001 TYR A 104 PHE 0.011 0.001 PHE A 577 TRP 0.034 0.002 TRP A 472 HIS 0.003 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8370) covalent geometry : angle 0.56127 (11362) hydrogen bonds : bond 0.02975 ( 526) hydrogen bonds : angle 3.57316 ( 1554) Misc. bond : bond 0.00437 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2242.52 seconds wall clock time: 39 minutes 12.49 seconds (2352.49 seconds total)