Starting phenix.real_space_refine on Fri Jul 3 22:33:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.map" model { file = "/net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihd_52865/07_2026/9ihd_52865.cif" } resolution = 2.97 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= 1.000 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 Fe 1 7.16 5 P 290 5.49 5 S 41 5.16 5 C 9483 2.51 5 N 3075 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16508 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.02, per 1000 atoms: 0.18 Number of scatterers: 16508 At special positions: 0 Unit cell: (119.68, 121.04, 133.96, 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) Fe 1 26.01 S 41 16.00 P 290 15.00 O 3618 8.00 N 3075 7.00 C 9483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied NAG-ASN " NAG N 603 " - " ASN N 189 " " NAG N 604 " - " ASN N 317 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 537.9 milliseconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 60.6% alpha, 3.0% beta 134 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.121A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.547A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.877A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.994A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.506A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.671A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.560A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.560A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.720A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.700A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 180 through 188 Processing helix chain 'N' and resid 219 through 225 removed outlier: 3.951A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 310 removed outlier: 5.312A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Proline residue: N 303 - end of helix Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.601A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 399 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 440 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.672A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 removed outlier: 3.633A pdb=" N THR N 541 " --> pdb=" O ILE N 537 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 576 removed outlier: 4.210A pdb=" N SER N 574 " --> pdb=" O ASN N 571 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.151A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.160A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.725A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.010A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.158A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 27 through 28 removed outlier: 3.692A pdb=" N ARG M 27 " --> pdb=" O ASN N 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'M' and resid 78 through 83 removed outlier: 3.970A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AB5, first strand: chain 'N' and resid 546 through 547 555 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 6760 1.39 - 1.57: 10016 1.57 - 1.75: 578 1.75 - 1.93: 69 1.93 - 2.11: 4 Bond restraints: 17427 Sorted by residual: bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DC J 44 " pdb=" C2' DC J 44 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.06e+00 bond pdb=" C3' DA J 63 " pdb=" C2' DA J 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 bond pdb=" C3' DC J -21 " pdb=" C2' DC J -21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.34e+00 ... (remaining 17422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 24686 2.88 - 5.77: 127 5.77 - 8.65: 8 8.65 - 11.53: 3 11.53 - 14.41: 2 Bond angle restraints: 24826 Sorted by residual: angle pdb=" O4' DC J -48 " pdb=" C4' DC J -48 " pdb=" C3' DC J -48 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" N ASN N 189 " pdb=" CA ASN N 189 " pdb=" C ASN N 189 " ideal model delta sigma weight residual 110.65 104.72 5.93 1.26e+00 6.30e-01 2.21e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 ... (remaining 24821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8241 35.32 - 70.65: 1542 70.65 - 105.97: 17 105.97 - 141.30: 2 141.30 - 176.62: 6 Dihedral angle restraints: 9808 sinusoidal: 5996 harmonic: 3812 Sorted by residual: dihedral pdb=" C4' DC J 44 " pdb=" C3' DC J 44 " pdb=" O3' DC J 44 " pdb=" P DC J 45 " ideal model delta sinusoidal sigma weight residual -140.00 36.62 -176.62 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J -21 " pdb=" C3' DC J -21 " pdb=" O3' DC J -21 " pdb=" P DC J -20 " ideal model delta sinusoidal sigma weight residual 220.00 54.93 165.07 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -31 " pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " pdb=" P DG J -30 " ideal model delta sinusoidal sigma weight residual 220.00 63.87 156.13 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2768 0.125 - 0.249: 14 0.249 - 0.374: 0 0.374 - 0.499: 0 0.499 - 0.623: 1 Chirality restraints: 2783 Sorted by residual: chirality pdb=" C1 NAG N 603 " pdb=" ND2 ASN N 189 " pdb=" C2 NAG N 603 " pdb=" O5 NAG N 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" C3' DC J 44 " pdb=" C4' DC J 44 " pdb=" O3' DC J 44 " pdb=" C2' DC J 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA GLU M 67 " pdb=" N GLU M 67 " pdb=" C GLU M 67 " pdb=" CB GLU M 67 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2780 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 333 " -0.522 9.50e-02 1.11e+02 2.34e-01 3.36e+01 pdb=" NE ARG N 333 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG N 333 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG N 333 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG N 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 189 " -0.026 2.00e-02 2.50e+03 2.52e-02 7.93e+00 pdb=" CG ASN N 189 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN N 189 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN N 189 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG N 603 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 108 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C VAL H 108 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL H 108 " -0.011 2.00e-02 2.50e+03 pdb=" N SER H 109 " -0.010 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 875 2.72 - 3.27: 14329 3.27 - 3.81: 30007 3.81 - 4.36: 37841 4.36 - 4.90: 56974 Nonbonded interactions: 140026 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.177 3.120 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR C 76 " model vdw 2.190 3.040 nonbonded pdb=" NH1 ARG M 62 " pdb=" OD2 ASP N 416 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG N 333 " pdb=" O2A HEM N 601 " model vdw 2.264 2.496 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.266 3.040 ... (remaining 140021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.425 17435 Z= 0.444 Angle : 0.718 14.414 24838 Z= 0.584 Chirality : 0.044 0.623 2783 Planarity : 0.007 0.234 2169 Dihedral : 26.624 176.619 7335 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.78 % Allowed : 23.90 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.52 (0.24), residues: 1293 helix: 1.90 (0.20), residues: 737 sheet: None (None), residues: 0 loop : -0.17 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 185 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE N 332 TRP 0.007 0.001 TRP M 89 HIS 0.002 0.000 HIS M 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.44 (17427) covalent geometry : angle 0.71241 / 0.58 (24826) SS BOND : bond 0.00208 / 0.12 ( 3) SS BOND : angle 0.80055 / 0.43 ( 6) hydrogen bonds : bond 0.12352 / 8.48 ( 900) hydrogen bonds : angle 4.69170 / 3.35 ( 2303) Misc. bond : bond 0.24531 / 11.68 ( 3) link_NAG-ASN : bond 0.01147 / 0.76 ( 2) link_NAG-ASN : angle 6.00863 / 3.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8352 (tttt) cc_final: 0.7925 (tttm) REVERT: A 115 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8145 (mttp) REVERT: A 129 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7210 (tmt170) REVERT: C 15 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8140 (ptmm) REVERT: D 32 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7286 (pt0) REVERT: E 59 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: E 120 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: F 44 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8435 (tttm) REVERT: G 74 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: G 95 LYS cc_start: 0.8766 (tttt) cc_final: 0.8382 (ttmt) REVERT: G 108 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8610 (mp) REVERT: H 83 ARG cc_start: 0.8451 (mmt-90) cc_final: 0.7996 (mmt90) REVERT: M 27 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8453 (mtp85) REVERT: M 67 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: N 140 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: N 185 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7866 (ttp-110) REVERT: N 210 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7359 (mp) REVERT: N 249 MET cc_start: 0.8813 (mmm) cc_final: 0.8579 (mmt) REVERT: N 462 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7915 (mtt90) REVERT: N 504 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: N 526 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6859 (mp10) outliers start: 31 outliers final: 18 residues processed: 166 average time/residue: 0.6743 time to fit residues: 121.7784 Evaluate side-chains 168 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 547 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.0060 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120929 restraints weight = 17806.550| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.23 r_work: 0.3337 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.376 17435 Z= 0.163 Angle : 0.633 16.316 24838 Z= 0.347 Chirality : 0.046 0.552 2783 Planarity : 0.005 0.092 2169 Dihedral : 29.048 174.273 4769 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.31 % Allowed : 22.38 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 1.78 (0.24), residues: 1293 helix: 2.21 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.28 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 185 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP N 436 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (17427) covalent geometry : angle 0.62376 / 0.35 (24826) SS BOND : bond 0.00401 / 0.22 ( 3) SS BOND : angle 0.43172 / 0.31 ( 6) hydrogen bonds : bond 0.05468 / 3.69 ( 900) hydrogen bonds : angle 3.48640 / 2.51 ( 2303) Misc. bond : bond 0.21735 / 10.35 ( 3) link_NAG-ASN : bond 0.01857 / 1.24 ( 2) link_NAG-ASN : angle 6.85494 / 4.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8085 (tttt) cc_final: 0.7712 (tttm) REVERT: A 129 ARG cc_start: 0.8204 (ttt180) cc_final: 0.7921 (tmt170) REVERT: C 15 LYS cc_start: 0.8400 (mtmm) cc_final: 0.8175 (ptmm) REVERT: D 32 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7253 (pt0) REVERT: E 131 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: F 92 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7916 (ttp80) REVERT: G 74 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8375 (mtmm) REVERT: G 92 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: G 95 LYS cc_start: 0.8806 (tttt) cc_final: 0.8556 (ttmt) REVERT: G 108 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (mp) REVERT: H 30 ARG cc_start: 0.7989 (mmt90) cc_final: 0.6818 (mtp-110) REVERT: H 83 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8382 (mmt-90) REVERT: H 90 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: M 27 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8251 (mtp85) REVERT: N 210 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7243 (mp) REVERT: N 249 MET cc_start: 0.8663 (mmm) cc_final: 0.8428 (mmt) outliers start: 37 outliers final: 11 residues processed: 171 average time/residue: 0.6825 time to fit residues: 127.4648 Evaluate side-chains 159 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 153 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 125 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122775 restraints weight = 17987.358| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.23 r_work: 0.3363 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.365 17435 Z= 0.137 Angle : 0.592 14.929 24838 Z= 0.327 Chirality : 0.044 0.459 2783 Planarity : 0.004 0.088 2169 Dihedral : 29.122 172.461 4717 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.31 % Allowed : 22.74 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.01 (0.24), residues: 1293 helix: 2.45 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.25 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 185 TYR 0.009 0.001 TYR D 34 PHE 0.008 0.001 PHE M 86 TRP 0.007 0.001 TRP N 436 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (17427) covalent geometry : angle 0.58458 / 0.33 (24826) SS BOND : bond 0.00311 / 0.19 ( 3) SS BOND : angle 0.64607 / 0.42 ( 6) hydrogen bonds : bond 0.04838 / 3.27 ( 900) hydrogen bonds : angle 3.27406 / 2.37 ( 2303) Misc. bond : bond 0.21072 / 10.03 ( 3) link_NAG-ASN : bond 0.01609 / 1.07 ( 2) link_NAG-ASN : angle 6.16199 / 3.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7958 (tttt) cc_final: 0.7574 (tttm) REVERT: A 129 ARG cc_start: 0.8201 (ttt180) cc_final: 0.7878 (tmt170) REVERT: C 15 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8126 (ptmm) REVERT: D 32 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7267 (pt0) REVERT: F 92 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: G 74 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8332 (mtmm) REVERT: G 92 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7480 (mm-30) REVERT: G 95 LYS cc_start: 0.8788 (tttt) cc_final: 0.8536 (ttmt) REVERT: G 108 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8643 (mp) REVERT: H 83 ARG cc_start: 0.8573 (mmt-90) cc_final: 0.8204 (mmt90) REVERT: H 90 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: M 27 ARG cc_start: 0.8807 (mmm160) cc_final: 0.8284 (mtp85) REVERT: M 52 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7356 (mttp) REVERT: M 53 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7103 (ttm170) REVERT: N 185 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7774 (ttp-110) REVERT: N 210 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7226 (mp) REVERT: N 249 MET cc_start: 0.8607 (mmm) cc_final: 0.8387 (mmt) REVERT: N 526 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6775 (mp10) outliers start: 37 outliers final: 15 residues processed: 168 average time/residue: 0.7070 time to fit residues: 128.9554 Evaluate side-chains 166 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 73 ASN E 125 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123412 restraints weight = 17787.020| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.21 r_work: 0.3371 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.365 17435 Z= 0.129 Angle : 0.591 15.003 24838 Z= 0.325 Chirality : 0.044 0.425 2783 Planarity : 0.004 0.086 2169 Dihedral : 29.123 172.485 4712 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.95 % Allowed : 23.01 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.12 (0.24), residues: 1293 helix: 2.56 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.24 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 202 TYR 0.008 0.001 TYR D 34 PHE 0.008 0.001 PHE M 86 TRP 0.007 0.001 TRP N 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (17427) covalent geometry : angle 0.58385 / 0.32 (24826) SS BOND : bond 0.00316 / 0.18 ( 3) SS BOND : angle 0.50240 / 0.38 ( 6) hydrogen bonds : bond 0.04673 / 3.16 ( 900) hydrogen bonds : angle 3.22311 / 2.34 ( 2303) Misc. bond : bond 0.21089 / 10.04 ( 3) link_NAG-ASN : bond 0.01438 / 0.96 ( 2) link_NAG-ASN : angle 6.05559 / 3.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7924 (tttt) cc_final: 0.7618 (tttm) REVERT: A 120 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8747 (mtt) REVERT: A 129 ARG cc_start: 0.8189 (ttt180) cc_final: 0.7866 (tmt170) REVERT: C 15 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8142 (ptmm) REVERT: D 32 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7259 (pt0) REVERT: E 131 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7311 (mtp85) REVERT: F 92 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: G 74 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8325 (mtmm) REVERT: G 95 LYS cc_start: 0.8784 (tttt) cc_final: 0.8537 (ttmt) REVERT: G 108 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8639 (mp) REVERT: H 83 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8192 (mmt90) REVERT: H 90 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: M 27 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8289 (mtp85) REVERT: M 52 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7396 (mttp) REVERT: M 53 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: N 185 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7786 (ttp-110) REVERT: N 210 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7223 (mp) REVERT: N 249 MET cc_start: 0.8604 (mmm) cc_final: 0.8378 (mmt) REVERT: N 526 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6761 (mp10) outliers start: 33 outliers final: 16 residues processed: 168 average time/residue: 0.6943 time to fit residues: 126.7417 Evaluate side-chains 169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** N 201 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 = 0.4001 r_free = 0.4001 target = 0.159479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122537 restraints weight = 17785.424| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.22 r_work: 0.3358 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.349 17435 Z= 0.143 Angle : 0.592 15.517 24838 Z= 0.323 Chirality : 0.044 0.386 2783 Planarity : 0.004 0.092 2169 Dihedral : 29.207 172.176 4712 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.39 % Allowed : 21.40 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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 (0.24), residues: 1293 helix: 2.56 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.30 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 202 TYR 0.010 0.001 TYR D 34 PHE 0.008 0.001 PHE E 67 TRP 0.007 0.001 TRP N 436 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (17427) covalent geometry : angle 0.58507 / 0.32 (24826) SS BOND : bond 0.00370 / 0.20 ( 3) SS BOND : angle 0.58941 / 0.40 ( 6) hydrogen bonds : bond 0.04761 / 3.22 ( 900) hydrogen bonds : angle 3.15723 / 2.29 ( 2303) Misc. bond : bond 0.20173 / 9.61 ( 3) link_NAG-ASN : bond 0.01261 / 0.84 ( 2) link_NAG-ASN : angle 5.65056 / 3.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7902 (tttt) cc_final: 0.7603 (tttm) REVERT: A 120 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8772 (mtt) REVERT: A 129 ARG cc_start: 0.8187 (ttt180) cc_final: 0.7857 (tmt170) REVERT: C 15 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8145 (ptmm) REVERT: D 32 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7265 (pt0) REVERT: E 59 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: E 131 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7411 (mtp85) REVERT: F 92 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7982 (ttp80) REVERT: G 74 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8286 (mtmm) REVERT: G 92 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: G 95 LYS cc_start: 0.8770 (tttt) cc_final: 0.8531 (ttmt) REVERT: G 108 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8636 (mp) REVERT: H 83 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8358 (mmt-90) REVERT: H 90 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: M 27 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8233 (mtp85) REVERT: N 185 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7764 (ttp-110) REVERT: N 249 MET cc_start: 0.8607 (mmm) cc_final: 0.8394 (mmt) REVERT: N 259 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7201 (ttp-170) REVERT: N 526 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: N 530 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8245 (mt0) outliers start: 49 outliers final: 20 residues processed: 176 average time/residue: 0.6654 time to fit residues: 127.5956 Evaluate side-chains 169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 0.0050 chunk 104 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 73 ASN E 125 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122982 restraints weight = 17751.839| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.24 r_work: 0.3367 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.350 17435 Z= 0.127 Angle : 0.587 15.352 24838 Z= 0.322 Chirality : 0.043 0.383 2783 Planarity : 0.004 0.089 2169 Dihedral : 29.202 172.205 4710 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.22 % Allowed : 22.65 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.13 (0.24), residues: 1293 helix: 2.60 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.29 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 202 TYR 0.009 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (17427) covalent geometry : angle 0.58100 / 0.32 (24826) SS BOND : bond 0.00300 / 0.17 ( 3) SS BOND : angle 0.45881 / 0.34 ( 6) hydrogen bonds : bond 0.04639 / 3.14 ( 900) hydrogen bonds : angle 3.14295 / 2.28 ( 2303) Misc. bond : bond 0.20189 / 9.61 ( 3) link_NAG-ASN : bond 0.01343 / 0.90 ( 2) link_NAG-ASN : angle 5.59555 / 3.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8755 (mtt) REVERT: A 129 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7866 (tmt170) REVERT: C 15 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8142 (ptmm) REVERT: D 32 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7286 (pt0) REVERT: E 59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: F 92 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: G 74 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8275 (mtmm) REVERT: G 92 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: G 95 LYS cc_start: 0.8761 (tttt) cc_final: 0.8514 (ttmt) REVERT: G 108 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8657 (mp) REVERT: H 83 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.8350 (mmt-90) REVERT: H 90 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: M 27 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8212 (mtp85) REVERT: N 185 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7714 (ttp-110) REVERT: N 249 MET cc_start: 0.8590 (mmm) cc_final: 0.8372 (mmt) REVERT: N 259 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7298 (ttp-170) REVERT: N 526 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: N 530 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8234 (mt0) outliers start: 36 outliers final: 22 residues processed: 162 average time/residue: 0.7026 time to fit residues: 123.3356 Evaluate side-chains 170 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123090 restraints weight = 17771.530| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.22 r_work: 0.3381 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.352 17435 Z= 0.133 Angle : 0.585 15.004 24838 Z= 0.321 Chirality : 0.043 0.376 2783 Planarity : 0.004 0.090 2169 Dihedral : 29.204 172.010 4710 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.22 % Allowed : 22.65 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.14 (0.24), residues: 1293 helix: 2.60 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.30 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 307 TYR 0.009 0.001 TYR D 34 PHE 0.008 0.001 PHE M 86 TRP 0.007 0.001 TRP N 436 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (17427) covalent geometry : angle 0.57883 / 0.32 (24826) SS BOND : bond 0.00400 / 0.21 ( 3) SS BOND : angle 0.47088 / 0.35 ( 6) hydrogen bonds : bond 0.04635 / 3.14 ( 900) hydrogen bonds : angle 3.12640 / 2.27 ( 2303) Misc. bond : bond 0.20319 / 9.68 ( 3) link_NAG-ASN : bond 0.01215 / 0.81 ( 2) link_NAG-ASN : angle 5.52454 / 3.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8758 (mtt) REVERT: A 129 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7859 (tmt170) REVERT: C 15 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8147 (ptmm) REVERT: D 32 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7277 (pt0) REVERT: E 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: E 131 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7386 (mtp85) REVERT: F 92 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: G 74 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8277 (mtmm) REVERT: G 92 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: G 95 LYS cc_start: 0.8773 (tttt) cc_final: 0.8524 (ttmt) REVERT: G 108 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8632 (mp) REVERT: H 83 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8350 (mmt-90) REVERT: H 90 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: M 27 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8219 (mtp85) REVERT: N 185 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7707 (ttp-110) REVERT: N 249 MET cc_start: 0.8600 (mmm) cc_final: 0.8378 (mmt) REVERT: N 259 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7205 (ttp-170) REVERT: N 526 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: N 530 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8274 (mt0) outliers start: 36 outliers final: 21 residues processed: 162 average time/residue: 0.7548 time to fit residues: 132.8936 Evaluate side-chains 169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121437 restraints weight = 17861.690| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.22 r_work: 0.3342 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.323 17435 Z= 0.163 Angle : 0.602 16.142 24838 Z= 0.328 Chirality : 0.044 0.374 2783 Planarity : 0.005 0.098 2169 Dihedral : 29.264 172.022 4710 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.04 % Allowed : 22.83 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.00 (0.24), residues: 1293 helix: 2.49 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.36 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 62 TYR 0.013 0.001 TYR N 334 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP N 436 HIS 0.003 0.001 HIS M 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (17427) covalent geometry : angle 0.59624 / 0.33 (24826) SS BOND : bond 0.00349 / 0.19 ( 3) SS BOND : angle 0.88004 / 0.51 ( 6) hydrogen bonds : bond 0.04982 / 3.37 ( 900) hydrogen bonds : angle 3.18522 / 2.32 ( 2303) Misc. bond : bond 0.18632 / 8.87 ( 3) link_NAG-ASN : bond 0.00989 / 0.66 ( 2) link_NAG-ASN : angle 5.42500 / 3.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7925 (tttt) cc_final: 0.7627 (tttm) REVERT: A 129 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7907 (tmt170) REVERT: C 15 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8160 (ptmm) REVERT: D 32 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7306 (pt0) REVERT: E 59 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: E 131 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7401 (mtp85) REVERT: G 74 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8282 (mtmm) REVERT: G 95 LYS cc_start: 0.8788 (tttt) cc_final: 0.8547 (ttmt) REVERT: G 108 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8643 (mp) REVERT: H 83 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.8380 (mmt-90) REVERT: H 90 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: M 27 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8204 (mtp85) REVERT: N 185 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7701 (ttp-110) REVERT: N 192 ASN cc_start: 0.7675 (m-40) cc_final: 0.7465 (m-40) REVERT: N 249 MET cc_start: 0.8631 (mmm) cc_final: 0.8418 (mmt) REVERT: N 259 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7267 (ttp-170) REVERT: N 526 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: N 530 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8250 (mt0) outliers start: 34 outliers final: 21 residues processed: 163 average time/residue: 0.7069 time to fit residues: 125.6579 Evaluate side-chains 165 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 0.2980 chunk 112 optimal weight: 0.0030 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 125 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122606 restraints weight = 17760.814| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.23 r_work: 0.3368 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.328 17435 Z= 0.127 Angle : 0.595 15.649 24838 Z= 0.325 Chirality : 0.043 0.359 2783 Planarity : 0.004 0.089 2169 Dihedral : 29.250 172.576 4710 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.78 % Allowed : 23.10 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.07 (0.24), residues: 1293 helix: 2.55 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 307 TYR 0.010 0.001 TYR N 334 PHE 0.010 0.001 PHE E 67 TRP 0.009 0.001 TRP M 89 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.13 (17427) covalent geometry : angle 0.58885 / 0.32 (24826) SS BOND : bond 0.00178 / 0.11 ( 3) SS BOND : angle 0.67444 / 0.40 ( 6) hydrogen bonds : bond 0.04650 / 3.14 ( 900) hydrogen bonds : angle 3.16361 / 2.30 ( 2303) Misc. bond : bond 0.18942 / 9.02 ( 3) link_NAG-ASN : bond 0.01208 / 0.81 ( 2) link_NAG-ASN : angle 5.35184 / 3.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7845 (tmt170) REVERT: C 15 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8139 (ptmm) REVERT: D 32 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7297 (pt0) REVERT: E 59 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: E 131 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7386 (mtp85) REVERT: G 74 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8268 (mtmm) REVERT: G 95 LYS cc_start: 0.8760 (tttt) cc_final: 0.8518 (ttmt) REVERT: G 108 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8660 (mp) REVERT: H 83 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8353 (mmt-90) REVERT: H 90 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: M 27 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8197 (mtp85) REVERT: N 185 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7701 (ttp-110) REVERT: N 249 MET cc_start: 0.8604 (mmm) cc_final: 0.8385 (mmt) REVERT: N 259 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7251 (ttp-170) REVERT: N 526 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: N 530 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: N 539 ASP cc_start: 0.7549 (t0) cc_final: 0.7304 (t0) outliers start: 31 outliers final: 19 residues processed: 161 average time/residue: 0.7190 time to fit residues: 125.9721 Evaluate side-chains 163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 53 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 chunk 61 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 73 ASN E 125 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122550 restraints weight = 17802.045| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.22 r_work: 0.3370 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.335 17435 Z= 0.132 Angle : 0.595 15.145 24838 Z= 0.323 Chirality : 0.044 0.421 2783 Planarity : 0.004 0.091 2169 Dihedral : 29.254 172.165 4710 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.60 % Allowed : 23.46 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.06 (0.24), residues: 1293 helix: 2.54 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.36 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 333 TYR 0.009 0.001 TYR D 34 PHE 0.009 0.001 PHE M 86 TRP 0.008 0.001 TRP M 89 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (17427) covalent geometry : angle 0.58876 / 0.32 (24826) SS BOND : bond 0.00316 / 0.18 ( 3) SS BOND : angle 0.63773 / 0.42 ( 6) hydrogen bonds : bond 0.04698 / 3.18 ( 900) hydrogen bonds : angle 3.14638 / 2.29 ( 2303) Misc. bond : bond 0.19366 / 9.22 ( 3) link_NAG-ASN : bond 0.00888 / 0.59 ( 2) link_NAG-ASN : angle 5.34808 / 3.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7851 (tmt170) REVERT: C 15 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8127 (ptmm) REVERT: D 32 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7305 (pt0) REVERT: E 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: E 131 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7371 (mtp85) REVERT: F 92 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: G 74 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8273 (mtmm) REVERT: G 95 LYS cc_start: 0.8766 (tttt) cc_final: 0.8522 (ttmt) REVERT: G 108 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8635 (mp) REVERT: H 83 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8362 (mmt-90) REVERT: H 90 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: M 27 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8198 (mtp85) REVERT: N 185 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7699 (ttp-110) REVERT: N 249 MET cc_start: 0.8603 (mmm) cc_final: 0.8388 (mmt) REVERT: N 259 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7271 (ttp-170) REVERT: N 526 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: N 530 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: N 539 ASP cc_start: 0.7556 (t0) cc_final: 0.7333 (t0) outliers start: 29 outliers final: 18 residues processed: 157 average time/residue: 0.8183 time to fit residues: 139.9008 Evaluate side-chains 164 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122670 restraints weight = 17764.717| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.22 r_work: 0.3370 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.336 17435 Z= 0.129 Angle : 0.590 15.045 24838 Z= 0.322 Chirality : 0.043 0.338 2783 Planarity : 0.004 0.091 2169 Dihedral : 29.252 172.176 4710 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.51 % Allowed : 23.63 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 2.07 (0.24), residues: 1293 helix: 2.55 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 333 TYR 0.009 0.001 TYR D 34 PHE 0.009 0.001 PHE M 86 TRP 0.008 0.001 TRP M 89 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (17427) covalent geometry : angle 0.58453 / 0.32 (24826) SS BOND : bond 0.00390 / 0.21 ( 3) SS BOND : angle 0.56784 / 0.38 ( 6) hydrogen bonds : bond 0.04670 / 3.16 ( 900) hydrogen bonds : angle 3.14343 / 2.29 ( 2303) Misc. bond : bond 0.19421 / 9.25 ( 3) link_NAG-ASN : bond 0.01185 / 0.79 ( 2) link_NAG-ASN : angle 5.36500 / 3.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.32 seconds wall clock time: 87 minutes 15.18 seconds (5235.18 seconds total)