Starting phenix.real_space_refine on Thu Aug 6 05:42:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yi_75530/08_2026/10yi_75530.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 1.034 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: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 25 5.16 5 C 7679 2.51 5 N 2529 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13642 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2722 Classifications: {'DNA': 132} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 131} Chain: "L" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1661 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 195} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.17 Number of scatterers: 13642 At special positions: 0 Unit cell: (90.628, 122.576, 138.876, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 295 15.00 O 3114 8.00 N 2529 7.00 C 7679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 319.3 milliseconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1788 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 63.6% alpha, 10.6% beta 147 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.205A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.592A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.568A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.711A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.568A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.357A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.560A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.264A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.616A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.576A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.355A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.555A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'L' and resid 404 through 412 Processing helix chain 'L' and resid 447 through 453 removed outlier: 3.894A pdb=" N HIS L 453 " --> pdb=" O HIS L 449 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 486 through 490 removed outlier: 3.571A pdb=" N THR L 489 " --> pdb=" O PRO L 486 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L 490 " --> pdb=" O PHE L 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 486 through 490' Processing helix chain 'L' and resid 522 through 534 Processing helix chain 'L' and resid 551 through 564 removed outlier: 4.260A pdb=" N MET L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN L 564 " --> pdb=" O THR L 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A 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 removed outlier: 6.432A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 'E' and resid 83 through 84 removed outlier: 7.063A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.203A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'L' and resid 398 through 401 removed outlier: 7.129A pdb=" N LEU L 398 " --> pdb=" O TRP L 586 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS L 588 " --> pdb=" O LEU L 398 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU L 400 " --> pdb=" O LYS L 588 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LYS L 590 " --> pdb=" O GLU L 400 " (cutoff:3.500A) removed outlier: 10.733A pdb=" N HIS L 585 " --> pdb=" O ASP L 574 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP L 574 " --> pdb=" O HIS L 585 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 436 through 439 removed outlier: 7.027A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 483 through 485 removed outlier: 3.727A pdb=" N LYS L 483 " --> pdb=" O ASP L 478 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 476 " --> pdb=" O LEU L 485 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET L 542 " --> pdb=" O VAL L 503 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU L 505 " --> pdb=" O MET L 542 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1986 1.33 - 1.45: 4996 1.45 - 1.57: 6883 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14496 Sorted by residual: bond pdb=" C GLU L 580 " pdb=" N PRO L 581 " ideal model delta sigma weight residual 1.335 1.369 -0.034 8.70e-03 1.32e+04 1.49e+01 bond pdb=" C PRO G 26 " pdb=" O PRO G 26 " ideal model delta sigma weight residual 1.235 1.206 0.029 7.90e-03 1.60e+04 1.39e+01 bond pdb=" C3' DG K 52 " pdb=" C2' DG K 52 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I 135 " pdb=" C2' DA I 135 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C3' DT K 96 " pdb=" C2' DT K 96 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 19419 1.47 - 2.95: 1344 2.95 - 4.42: 60 4.42 - 5.90: 7 5.90 - 7.37: 6 Bond angle restraints: 20836 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 104 " pdb=" C4 DT I 104 " pdb=" O4 DT I 104 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT K 105 " pdb=" C4 DT K 105 " pdb=" O4 DT K 105 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 20831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 6213 29.04 - 58.08: 1646 58.08 - 87.13: 101 87.13 - 116.17: 0 116.17 - 145.21: 2 Dihedral angle restraints: 7962 sinusoidal: 5190 harmonic: 2772 Sorted by residual: dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DG K 82 " pdb=" C3' DG K 82 " pdb=" O3' DG K 82 " pdb=" P DT K 83 " ideal model delta sinusoidal sigma weight residual 220.00 74.79 145.21 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 7959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1529 0.039 - 0.077: 624 0.077 - 0.116: 181 0.116 - 0.154: 23 0.154 - 0.193: 3 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ILE L 420 " pdb=" N ILE L 420 " pdb=" C ILE L 420 " pdb=" CB ILE L 420 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA LYS L 421 " pdb=" N LYS L 421 " pdb=" C LYS L 421 " pdb=" CB LYS L 421 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' DC K 126 " pdb=" C4' DC K 126 " pdb=" O3' DC K 126 " pdb=" C2' DC K 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 2357 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 43 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 80 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 580 " 0.029 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO L 581 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 581 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 581 " 0.025 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 6749 3.03 - 3.49: 13248 3.49 - 3.96: 27029 3.96 - 4.43: 30460 4.43 - 4.90: 40571 Nonbonded interactions: 118057 Sorted by model distance: nonbonded pdb=" O5' DG K 95 " pdb=" O4' DG K 95 " model vdw 2.557 2.432 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.594 2.672 nonbonded pdb=" N1 DG K 101 " pdb=" C4 DG K 101 " model vdw 2.595 2.672 nonbonded pdb=" N1 DG K 18 " pdb=" C4 DG K 18 " model vdw 2.595 2.672 nonbonded pdb=" N1 DG K 67 " pdb=" C4 DG K 67 " model vdw 2.595 2.672 ... (remaining 118052 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) 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: 4.340 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 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 0.037 14497 Z= 0.505 Angle : 0.737 7.371 20836 Z= 0.649 Chirality : 0.044 0.193 2360 Planarity : 0.005 0.051 1617 Dihedral : 26.243 145.211 6174 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.37 % Allowed : 4.10 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 938 helix: 0.20 (0.19), residues: 587 sheet: -0.96 (0.74), residues: 55 loop : -1.01 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.010 0.001 TYR L 512 PHE 0.015 0.001 PHE L 454 TRP 0.002 0.001 TRP L 586 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.51 (14496) covalent geometry : angle 0.73667 / 0.65 (20836) hydrogen bonds : bond 0.13918 / 9.20 ( 842) hydrogen bonds : angle 4.68286 / 3.34 ( 2147) Misc. bond : bond 0.00047 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8546 (mtm-85) REVERT: C 38 ASN cc_start: 0.8934 (m-40) cc_final: 0.8689 (m110) REVERT: C 72 ASP cc_start: 0.8466 (m-30) cc_final: 0.8196 (m-30) REVERT: C 73 ASN cc_start: 0.8741 (t0) cc_final: 0.8388 (t0) REVERT: D 85 LYS cc_start: 0.9332 (mmtt) cc_final: 0.9119 (mmtp) REVERT: E 79 LYS cc_start: 0.9035 (tttp) cc_final: 0.8786 (tttp) REVERT: G 92 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8859 (mm-30) REVERT: G 95 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9150 (tmtt) REVERT: G 104 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8623 (mm110) REVERT: L 397 MET cc_start: 0.8157 (tpp) cc_final: 0.6587 (mtp) REVERT: L 489 THR cc_start: 0.8659 (p) cc_final: 0.8061 (p) REVERT: L 493 HIS cc_start: 0.7746 (m90) cc_final: 0.7414 (m-70) REVERT: L 550 THR cc_start: 0.8393 (t) cc_final: 0.7754 (p) REVERT: L 586 TRP cc_start: 0.8626 (m-10) cc_final: 0.7895 (m-10) outliers start: 3 outliers final: 1 residues processed: 240 average time/residue: 0.7530 time to fit residues: 191.9883 Evaluate side-chains 188 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN B 93 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066268 restraints weight = 30990.949| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.56 r_work: 0.2782 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14497 Z= 0.148 Angle : 0.652 6.890 20836 Z= 0.380 Chirality : 0.045 0.231 2360 Planarity : 0.005 0.089 1617 Dihedral : 30.306 144.471 4276 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.36 % Allowed : 13.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 938 helix: 1.91 (0.21), residues: 592 sheet: 0.32 (0.79), residues: 44 loop : -0.95 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 426 TYR 0.013 0.001 TYR L 457 PHE 0.009 0.001 PHE L 417 TRP 0.003 0.001 TRP L 586 HIS 0.004 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (14496) covalent geometry : angle 0.65183 / 0.38 (20836) hydrogen bonds : bond 0.04850 / 3.26 ( 842) hydrogen bonds : angle 3.44627 / 2.42 ( 2147) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8812 (mtp180) cc_final: 0.8497 (mtm-85) REVERT: C 72 ASP cc_start: 0.8414 (m-30) cc_final: 0.8152 (m-30) REVERT: C 73 ASN cc_start: 0.8651 (t0) cc_final: 0.8225 (t0) REVERT: D 106 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8971 (mp) REVERT: E 133 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: G 95 LYS cc_start: 0.9373 (ttmt) cc_final: 0.9146 (tmtt) REVERT: L 397 MET cc_start: 0.7697 (tpp) cc_final: 0.7238 (mtp) REVERT: L 422 TYR cc_start: 0.8911 (m-10) cc_final: 0.8590 (m-10) REVERT: L 466 HIS cc_start: 0.8728 (p-80) cc_final: 0.8500 (p-80) REVERT: L 489 THR cc_start: 0.8631 (p) cc_final: 0.8089 (p) REVERT: L 493 HIS cc_start: 0.7654 (m90) cc_final: 0.7397 (m-70) REVERT: L 561 ARG cc_start: 0.9016 (tmt-80) cc_final: 0.8527 (ttp80) outliers start: 19 outliers final: 6 residues processed: 204 average time/residue: 0.7724 time to fit residues: 167.6372 Evaluate side-chains 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 519 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.101227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066624 restraints weight = 31187.938| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.58 r_work: 0.2780 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14497 Z= 0.152 Angle : 0.634 7.385 20836 Z= 0.368 Chirality : 0.044 0.225 2360 Planarity : 0.004 0.056 1617 Dihedral : 30.370 144.310 4276 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 15.16 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.27), residues: 938 helix: 2.38 (0.21), residues: 592 sheet: -0.28 (0.68), residues: 60 loop : -0.83 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 426 TYR 0.013 0.001 TYR L 593 PHE 0.009 0.001 PHE A 67 TRP 0.022 0.008 TRP L 586 HIS 0.007 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (14496) covalent geometry : angle 0.63440 / 0.37 (20836) hydrogen bonds : bond 0.04294 / 2.86 ( 842) hydrogen bonds : angle 3.34188 / 2.36 ( 2147) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8138 (m-30) REVERT: C 73 ASN cc_start: 0.8608 (t0) cc_final: 0.8182 (t0) REVERT: D 106 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8969 (mp) REVERT: E 120 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8596 (mtt) REVERT: E 133 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: G 95 LYS cc_start: 0.9363 (ttmt) cc_final: 0.9140 (tmtt) REVERT: L 400 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: L 419 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6924 (mm-30) REVERT: L 422 TYR cc_start: 0.8928 (m-10) cc_final: 0.8534 (m-80) REVERT: L 489 THR cc_start: 0.8616 (p) cc_final: 0.8055 (p) REVERT: L 493 HIS cc_start: 0.7599 (m90) cc_final: 0.7284 (m-70) REVERT: L 546 MET cc_start: 0.8657 (pmm) cc_final: 0.8125 (pmm) outliers start: 15 outliers final: 7 residues processed: 199 average time/residue: 0.7459 time to fit residues: 157.8536 Evaluate side-chains 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 423 ASP Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066623 restraints weight = 30982.493| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.58 r_work: 0.2786 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14497 Z= 0.141 Angle : 0.624 7.158 20836 Z= 0.361 Chirality : 0.043 0.221 2360 Planarity : 0.005 0.067 1617 Dihedral : 30.406 144.126 4276 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.86 % Allowed : 16.15 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.28), residues: 938 helix: 2.56 (0.21), residues: 592 sheet: -0.95 (0.66), residues: 61 loop : -0.85 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 561 TYR 0.013 0.001 TYR L 457 PHE 0.008 0.001 PHE A 67 TRP 0.011 0.004 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (14496) covalent geometry : angle 0.62384 / 0.36 (20836) hydrogen bonds : bond 0.03975 / 2.66 ( 842) hydrogen bonds : angle 3.27014 / 2.31 ( 2147) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8595 (t0) cc_final: 0.8162 (t0) REVERT: D 106 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8939 (mp) REVERT: E 120 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8583 (mtt) REVERT: E 133 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: G 95 LYS cc_start: 0.9387 (ttmt) cc_final: 0.9130 (tmtt) REVERT: L 400 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: L 409 MET cc_start: 0.8616 (tpt) cc_final: 0.8350 (mmt) REVERT: L 419 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6647 (mm-30) REVERT: L 422 TYR cc_start: 0.8921 (m-10) cc_final: 0.8457 (m-80) REVERT: L 489 THR cc_start: 0.8591 (p) cc_final: 0.7983 (p) REVERT: L 493 HIS cc_start: 0.7606 (m90) cc_final: 0.7280 (m-70) REVERT: L 546 MET cc_start: 0.8745 (pmm) cc_final: 0.8203 (pmm) outliers start: 15 outliers final: 7 residues processed: 192 average time/residue: 0.8218 time to fit residues: 167.8306 Evaluate side-chains 188 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 99 optimal weight: 50.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.101703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067355 restraints weight = 31202.660| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.60 r_work: 0.2808 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14497 Z= 0.134 Angle : 0.615 7.657 20836 Z= 0.357 Chirality : 0.042 0.219 2360 Planarity : 0.004 0.059 1617 Dihedral : 30.401 144.038 4276 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 16.27 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.28), residues: 938 helix: 2.69 (0.21), residues: 592 sheet: -0.88 (0.65), residues: 61 loop : -0.85 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 561 TYR 0.013 0.001 TYR L 579 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.002 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (14496) covalent geometry : angle 0.61509 / 0.36 (20836) hydrogen bonds : bond 0.03784 / 2.53 ( 842) hydrogen bonds : angle 3.20112 / 2.27 ( 2147) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8576 (t0) cc_final: 0.8133 (t0) REVERT: E 120 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8534 (mtt) REVERT: E 133 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: G 35 ARG cc_start: 0.9106 (mtm110) cc_final: 0.8816 (mtm110) REVERT: G 76 THR cc_start: 0.9252 (p) cc_final: 0.8953 (t) REVERT: G 95 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9128 (tmtt) REVERT: L 400 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: L 420 ILE cc_start: 0.9127 (mp) cc_final: 0.8879 (mm) REVERT: L 422 TYR cc_start: 0.8904 (m-10) cc_final: 0.8458 (m-80) REVERT: L 466 HIS cc_start: 0.8430 (p-80) cc_final: 0.8192 (p-80) REVERT: L 489 THR cc_start: 0.8616 (p) cc_final: 0.8037 (p) REVERT: L 493 HIS cc_start: 0.7585 (m90) cc_final: 0.7267 (m-70) outliers start: 20 outliers final: 5 residues processed: 201 average time/residue: 0.8075 time to fit residues: 173.1535 Evaluate side-chains 185 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 110 ASN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.064049 restraints weight = 30976.277| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.63 r_work: 0.2753 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14497 Z= 0.259 Angle : 0.693 9.424 20836 Z= 0.384 Chirality : 0.047 0.219 2360 Planarity : 0.005 0.053 1617 Dihedral : 30.649 144.376 4274 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.61 % Allowed : 16.77 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 938 helix: 2.47 (0.21), residues: 593 sheet: -0.86 (0.64), residues: 61 loop : -0.96 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 561 TYR 0.012 0.001 TYR L 579 PHE 0.013 0.002 PHE L 417 TRP 0.007 0.003 TRP L 586 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (14496) covalent geometry : angle 0.69342 / 0.38 (20836) hydrogen bonds : bond 0.04965 / 3.29 ( 842) hydrogen bonds : angle 3.37567 / 2.38 ( 2147) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8952 (mtpt) REVERT: C 72 ASP cc_start: 0.8312 (m-30) cc_final: 0.8091 (m-30) REVERT: C 73 ASN cc_start: 0.8653 (t0) cc_final: 0.8229 (t0) REVERT: D 106 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9065 (mp) REVERT: E 120 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8679 (mtt) REVERT: E 133 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: L 409 MET cc_start: 0.8539 (tpt) cc_final: 0.8296 (mmp) REVERT: L 420 ILE cc_start: 0.9133 (mp) cc_final: 0.8885 (mm) REVERT: L 422 TYR cc_start: 0.8892 (m-10) cc_final: 0.8502 (m-80) REVERT: L 479 ASN cc_start: 0.8802 (m-40) cc_final: 0.8513 (m110) REVERT: L 489 THR cc_start: 0.8608 (p) cc_final: 0.8058 (p) REVERT: L 493 HIS cc_start: 0.7485 (m90) cc_final: 0.7210 (m-70) outliers start: 21 outliers final: 7 residues processed: 190 average time/residue: 0.8231 time to fit residues: 166.4195 Evaluate side-chains 187 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 38 ASN G 110 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065548 restraints weight = 30804.721| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.62 r_work: 0.2790 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14497 Z= 0.141 Angle : 0.654 9.505 20836 Z= 0.367 Chirality : 0.045 0.225 2360 Planarity : 0.004 0.054 1617 Dihedral : 30.622 143.904 4274 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.49 % Allowed : 18.88 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 938 helix: 2.56 (0.21), residues: 593 sheet: -0.75 (0.64), residues: 61 loop : -0.89 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 42 TYR 0.010 0.001 TYR L 579 PHE 0.008 0.001 PHE L 417 TRP 0.008 0.003 TRP L 586 HIS 0.007 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (14496) covalent geometry : angle 0.65422 / 0.37 (20836) hydrogen bonds : bond 0.03997 / 2.66 ( 842) hydrogen bonds : angle 3.27664 / 2.31 ( 2147) Misc. bond : bond 0.00023 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8252 (m-30) cc_final: 0.8012 (m-30) REVERT: C 73 ASN cc_start: 0.8599 (t0) cc_final: 0.8152 (t0) REVERT: E 133 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: L 400 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: L 420 ILE cc_start: 0.9176 (mp) cc_final: 0.8928 (mm) REVERT: L 422 TYR cc_start: 0.8955 (m-10) cc_final: 0.8528 (m-80) REVERT: L 479 ASN cc_start: 0.8943 (m-40) cc_final: 0.8641 (m110) REVERT: L 493 HIS cc_start: 0.7658 (m90) cc_final: 0.7421 (m-70) outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.8750 time to fit residues: 171.2267 Evaluate side-chains 184 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 395 GLN Chi-restraints excluded: chain L residue 400 GLU Chi-restraints excluded: chain L residue 437 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 110 ASN F 25 ASN G 110 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065707 restraints weight = 30676.721| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.61 r_work: 0.2799 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14497 Z= 0.153 Angle : 0.642 10.476 20836 Z= 0.362 Chirality : 0.043 0.221 2360 Planarity : 0.004 0.052 1617 Dihedral : 30.573 143.773 4274 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.49 % Allowed : 19.01 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.28), residues: 938 helix: 2.62 (0.21), residues: 593 sheet: -0.63 (0.65), residues: 61 loop : -0.88 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 0.001 TYR L 579 PHE 0.009 0.001 PHE A 67 TRP 0.012 0.003 TRP L 586 HIS 0.003 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (14496) covalent geometry : angle 0.64190 / 0.36 (20836) hydrogen bonds : bond 0.03940 / 2.63 ( 842) hydrogen bonds : angle 3.25288 / 2.29 ( 2147) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8992 (m-30) cc_final: 0.8685 (m-30) REVERT: B 77 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8890 (mtpt) REVERT: B 93 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: C 73 ASN cc_start: 0.8641 (t0) cc_final: 0.8206 (t0) REVERT: E 133 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: L 422 TYR cc_start: 0.8855 (m-10) cc_final: 0.8538 (m-80) REVERT: L 479 ASN cc_start: 0.8817 (m-40) cc_final: 0.8556 (m110) REVERT: L 493 HIS cc_start: 0.7486 (m90) cc_final: 0.7274 (m-70) REVERT: L 519 MET cc_start: 0.8119 (pmm) cc_final: 0.7907 (pmm) outliers start: 12 outliers final: 4 residues processed: 182 average time/residue: 0.8712 time to fit residues: 168.6969 Evaluate side-chains 181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN ** L 430 HIS ** 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 = 0.3700 r_free = 0.3700 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067244 restraints weight = 30955.808| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.58 r_work: 0.2798 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14497 Z= 0.134 Angle : 0.641 11.025 20836 Z= 0.363 Chirality : 0.043 0.222 2360 Planarity : 0.004 0.050 1617 Dihedral : 30.503 143.654 4274 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.49 % Allowed : 19.25 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.28), residues: 938 helix: 2.71 (0.21), residues: 593 sheet: -0.66 (0.65), residues: 61 loop : -0.81 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 527 TYR 0.016 0.001 TYR L 579 PHE 0.008 0.001 PHE A 67 TRP 0.050 0.012 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (14496) covalent geometry : angle 0.64093 / 0.36 (20836) hydrogen bonds : bond 0.03734 / 2.51 ( 842) hydrogen bonds : angle 3.21832 / 2.26 ( 2147) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: C 72 ASP cc_start: 0.8258 (m-30) cc_final: 0.8022 (m-30) REVERT: C 73 ASN cc_start: 0.8606 (t0) cc_final: 0.8150 (t0) REVERT: E 120 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8540 (mtt) REVERT: E 133 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: G 76 THR cc_start: 0.9258 (p) cc_final: 0.8956 (t) REVERT: L 422 TYR cc_start: 0.8884 (m-10) cc_final: 0.8527 (m-80) REVERT: L 493 HIS cc_start: 0.7544 (m90) cc_final: 0.7304 (m-70) outliers start: 12 outliers final: 6 residues processed: 186 average time/residue: 0.8332 time to fit residues: 165.1344 Evaluate side-chains 183 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 17 optimal weight: 0.3980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 110 ASN G 110 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.101749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067444 restraints weight = 30926.779| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.57 r_work: 0.2829 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14497 Z= 0.139 Angle : 0.654 11.338 20836 Z= 0.369 Chirality : 0.042 0.221 2360 Planarity : 0.005 0.094 1617 Dihedral : 30.474 143.652 4274 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.99 % Allowed : 20.12 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.28), residues: 938 helix: 2.78 (0.21), residues: 592 sheet: -0.70 (0.67), residues: 61 loop : -0.86 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 527 TYR 0.019 0.001 TYR L 579 PHE 0.008 0.001 PHE A 67 TRP 0.032 0.008 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (14496) covalent geometry : angle 0.65390 / 0.37 (20836) hydrogen bonds : bond 0.03694 / 2.47 ( 842) hydrogen bonds : angle 3.20606 / 2.25 ( 2147) Misc. bond : bond 0.00002 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8259 (m-30) cc_final: 0.8019 (m-30) REVERT: C 73 ASN cc_start: 0.8589 (t0) cc_final: 0.8128 (t0) REVERT: D 63 ASN cc_start: 0.9026 (m-40) cc_final: 0.8706 (m110) REVERT: E 120 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: E 133 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: G 76 THR cc_start: 0.9252 (p) cc_final: 0.8949 (t) REVERT: L 409 MET cc_start: 0.8609 (tpt) cc_final: 0.8298 (mmm) REVERT: L 416 MET cc_start: 0.3164 (mpt) cc_final: 0.2857 (mpt) REVERT: L 419 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6536 (mm-30) REVERT: L 422 TYR cc_start: 0.8895 (m-10) cc_final: 0.8397 (m-80) REVERT: L 493 HIS cc_start: 0.7552 (m90) cc_final: 0.7302 (m-70) outliers start: 8 outliers final: 6 residues processed: 184 average time/residue: 0.8714 time to fit residues: 170.6232 Evaluate side-chains 185 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN ** L 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.101204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066649 restraints weight = 30959.680| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.63 r_work: 0.2797 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14497 Z= 0.167 Angle : 0.664 11.281 20836 Z= 0.374 Chirality : 0.043 0.221 2360 Planarity : 0.005 0.117 1617 Dihedral : 30.502 143.786 4274 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.12 % Allowed : 20.37 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.28), residues: 938 helix: 2.77 (0.21), residues: 592 sheet: -0.71 (0.68), residues: 61 loop : -0.91 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 527 TYR 0.019 0.001 TYR L 579 PHE 0.009 0.001 PHE D 65 TRP 0.018 0.005 TRP L 586 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (14496) covalent geometry : angle 0.66368 / 0.37 (20836) hydrogen bonds : bond 0.03855 / 2.57 ( 842) hydrogen bonds : angle 3.23371 / 2.28 ( 2147) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5595.36 seconds wall clock time: 95 minutes 37.33 seconds (5737.33 seconds total)