Starting phenix.real_space_refine on Fri Jul 3 11:00:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yi_75530/07_2026/10yi_75530.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yi_75530/07_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_75530/07_2026/10yi_75530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yi_75530/07_2026/10yi_75530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yi_75530/07_2026/10yi_75530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yi_75530/07_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): 0.01s 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: 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: 2.88, per 1000 atoms: 0.21 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: 1.11 Conformation dependent library (CDL) restraints added in 434.2 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: 1.92 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: 2.25 Time building geometry restraints manager: 1.44 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 - 1.84: 19957 1.84 - 3.69: 848 3.69 - 5.53: 22 5.53 - 7.38: 7 7.38 - 9.22: 2 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: 6212 29.04 - 58.08: 1647 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 - 0.046: 1708 0.046 - 0.092: 537 0.092 - 0.138: 111 0.138 - 0.184: 2 0.184 - 0.230: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" C3' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C4' AMP L1001 " pdb=" O3' AMP L1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.33e+00 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 ... (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: 0.010 Normalize map: mean=0, sd=1: 4.810 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.810 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- 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 9.223 20836 Z= 0.644 Chirality : 0.044 0.230 2360 Planarity : 0.005 0.051 1617 Dihedral : 26.246 145.211 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 0.00569 / 0.51 (14496) covalent geometry : angle 0.73692 / 0.64 (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 : 0.386 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: 0.8417 time to fit residues: 214.4753 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 : 0.389 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.100587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065982 restraints weight = 30958.529| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.56 r_work: 0.2774 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14497 Z= 0.153 Angle : 0.646 7.142 20836 Z= 0.380 Chirality : 0.045 0.216 2360 Planarity : 0.005 0.072 1617 Dihedral : 30.329 145.243 4276 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.86 % Allowed : 14.04 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 938 helix: 1.91 (0.21), residues: 592 sheet: 0.36 (0.81), residues: 44 loop : -0.96 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 426 TYR 0.013 0.001 TYR L 457 PHE 0.008 0.001 PHE B 61 TRP 0.005 0.001 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (14496) covalent geometry : angle 0.64638 / 0.38 (20836) hydrogen bonds : bond 0.05150 / 3.45 ( 842) hydrogen bonds : angle 3.50423 / 2.46 ( 2147) Misc. bond : bond 0.00012 / 0.01 ( 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 211 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8423 (m-30) cc_final: 0.8151 (m-30) REVERT: C 73 ASN cc_start: 0.8684 (t0) cc_final: 0.8267 (t0) REVERT: D 106 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8968 (mp) REVERT: E 133 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: G 95 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9148 (tmtt) REVERT: L 397 MET cc_start: 0.7667 (tpp) cc_final: 0.7058 (mtp) REVERT: L 422 TYR cc_start: 0.8897 (m-10) cc_final: 0.8577 (m-10) REVERT: L 466 HIS cc_start: 0.8637 (p-80) cc_final: 0.8416 (p-80) REVERT: L 489 THR cc_start: 0.8650 (p) cc_final: 0.8106 (p) REVERT: L 493 HIS cc_start: 0.7674 (m90) cc_final: 0.7414 (m-70) REVERT: L 561 ARG cc_start: 0.9053 (tmt-80) cc_final: 0.8542 (ttp80) REVERT: L 586 TRP cc_start: 0.8503 (m-10) cc_final: 0.7755 (m-10) outliers start: 15 outliers final: 5 residues processed: 201 average time/residue: 0.8974 time to fit residues: 191.6123 Evaluate side-chains 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 545 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.101299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066668 restraints weight = 31241.603| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.58 r_work: 0.2790 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14497 Z= 0.148 Angle : 0.629 8.966 20836 Z= 0.369 Chirality : 0.044 0.293 2360 Planarity : 0.005 0.055 1617 Dihedral : 30.419 144.634 4276 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 14.78 % Favored : 82.73 % 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: 1.89 (0.27), residues: 938 helix: 2.38 (0.21), residues: 592 sheet: -0.48 (0.66), residues: 60 loop : -0.82 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 42 TYR 0.011 0.001 TYR L 457 PHE 0.009 0.001 PHE A 67 TRP 0.004 0.001 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14496) covalent geometry : angle 0.62923 / 0.37 (20836) hydrogen bonds : bond 0.04221 / 2.83 ( 842) hydrogen bonds : angle 3.31765 / 2.34 ( 2147) Misc. bond : bond 0.00052 / 0.03 ( 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 218 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8392 (m-30) cc_final: 0.8127 (m-30) REVERT: C 73 ASN cc_start: 0.8597 (t0) cc_final: 0.8170 (t0) REVERT: D 42 TYR cc_start: 0.8718 (t80) cc_final: 0.8496 (t80) REVERT: D 106 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8940 (mp) REVERT: E 120 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8640 (mtt) REVERT: E 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: G 95 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9139 (tmtt) REVERT: L 397 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.6502 (mtp) REVERT: L 400 GLU cc_start: 0.8652 (tt0) cc_final: 0.8245 (tm-30) REVERT: L 422 TYR cc_start: 0.8886 (m-10) cc_final: 0.8526 (m-80) REVERT: L 423 ASP cc_start: 0.8186 (t70) cc_final: 0.7947 (p0) REVERT: L 489 THR cc_start: 0.8617 (p) cc_final: 0.8019 (p) REVERT: L 493 HIS cc_start: 0.7534 (m90) cc_final: 0.7224 (m-70) REVERT: L 586 TRP cc_start: 0.8591 (m-10) cc_final: 0.7929 (m-10) REVERT: L 587 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8210 (tm) outliers start: 20 outliers final: 7 residues processed: 205 average time/residue: 0.8723 time to fit residues: 190.2764 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 : 0.386 ------------------------------------------------------------------------------- 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 397 MET Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 519 MET Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 125 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066899 restraints weight = 30884.407| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.57 r_work: 0.2797 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1790 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= 0.140 Angle : 0.612 8.007 20836 Z= 0.357 Chirality : 0.042 0.206 2360 Planarity : 0.005 0.071 1617 Dihedral : 30.447 144.545 4276 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 2.03 (0.28), residues: 938 helix: 2.58 (0.21), residues: 592 sheet: -0.88 (0.65), residues: 62 loop : -0.85 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 561 TYR 0.012 0.001 TYR L 457 PHE 0.014 0.001 PHE L 417 TRP 0.003 0.001 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (14496) covalent geometry : angle 0.61219 / 0.36 (20836) hydrogen bonds : bond 0.03955 / 2.64 ( 842) hydrogen bonds : angle 3.24637 / 2.29 ( 2147) Misc. bond : bond 0.00025 / 0.02 ( 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 202 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8350 (m-30) cc_final: 0.8081 (m-30) REVERT: C 73 ASN cc_start: 0.8569 (t0) cc_final: 0.8145 (t0) REVERT: D 106 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8943 (mp) REVERT: E 120 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8572 (mtt) REVERT: E 133 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: G 35 ARG cc_start: 0.9109 (mtm110) cc_final: 0.8812 (mtm110) REVERT: G 76 THR cc_start: 0.9249 (p) cc_final: 0.8938 (t) REVERT: G 95 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9138 (tmtt) REVERT: L 397 MET cc_start: 0.8078 (tpp) cc_final: 0.7440 (mtp) REVERT: L 400 GLU cc_start: 0.8653 (tt0) cc_final: 0.8325 (tm-30) REVERT: L 489 THR cc_start: 0.8617 (p) cc_final: 0.8060 (p) REVERT: L 493 HIS cc_start: 0.7534 (m90) cc_final: 0.7226 (m-70) REVERT: L 550 THR cc_start: 0.8045 (p) cc_final: 0.7797 (t) REVERT: L 586 TRP cc_start: 0.8517 (m-10) cc_final: 0.7771 (m-10) outliers start: 15 outliers final: 7 residues processed: 192 average time/residue: 0.8726 time to fit residues: 178.3327 Evaluate side-chains 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 437 SER Chi-restraints excluded: chain L residue 519 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 99 optimal weight: 50.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.101849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067531 restraints weight = 31124.324| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.58 r_work: 0.2813 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1971 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= 0.133 Angle : 0.602 7.080 20836 Z= 0.352 Chirality : 0.042 0.204 2360 Planarity : 0.004 0.062 1617 Dihedral : 30.451 144.471 4276 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 16.27 % Favored : 81.37 % 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: 2.16 (0.28), residues: 938 helix: 2.70 (0.21), residues: 592 sheet: -0.82 (0.64), residues: 62 loop : -0.85 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 561 TYR 0.018 0.001 TYR L 422 PHE 0.010 0.001 PHE L 417 TRP 0.003 0.001 TRP L 586 HIS 0.003 0.000 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (14496) covalent geometry : angle 0.60196 / 0.35 (20836) hydrogen bonds : bond 0.03784 / 2.54 ( 842) hydrogen bonds : angle 3.18891 / 2.25 ( 2147) Misc. bond : bond 0.00018 / 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 213 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8568 (t0) cc_final: 0.8124 (t0) REVERT: E 120 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8537 (mtt) REVERT: E 133 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: G 35 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8795 (mtm110) REVERT: G 76 THR cc_start: 0.9249 (p) cc_final: 0.8953 (t) REVERT: G 95 LYS cc_start: 0.9383 (ttmt) cc_final: 0.9121 (tmtt) REVERT: L 397 MET cc_start: 0.8185 (tpp) cc_final: 0.6378 (mtp) REVERT: L 400 GLU cc_start: 0.8611 (tt0) cc_final: 0.8169 (tm-30) REVERT: L 466 HIS cc_start: 0.8412 (p-80) cc_final: 0.8179 (p-80) REVERT: L 471 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7304 (t0) REVERT: L 489 THR cc_start: 0.8627 (p) cc_final: 0.8055 (p) REVERT: L 493 HIS cc_start: 0.7527 (m90) cc_final: 0.7218 (m-70) REVERT: L 586 TRP cc_start: 0.8467 (m-10) cc_final: 0.7946 (m-10) REVERT: L 587 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8263 (tm) outliers start: 19 outliers final: 5 residues processed: 207 average time/residue: 0.8537 time to fit residues: 188.3615 Evaluate side-chains 188 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 416 MET Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 471 ASP Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 110 ASN G 110 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 585 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 = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065874 restraints weight = 30867.987| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.58 r_work: 0.2767 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14497 Z= 0.196 Angle : 0.638 8.424 20836 Z= 0.364 Chirality : 0.043 0.203 2360 Planarity : 0.005 0.053 1617 Dihedral : 30.548 144.679 4274 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.24 % Allowed : 17.02 % Favored : 80.75 % 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: 2.05 (0.28), residues: 938 helix: 2.63 (0.21), residues: 593 sheet: -1.10 (0.63), residues: 61 loop : -0.90 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 561 TYR 0.017 0.001 TYR L 422 PHE 0.009 0.001 PHE A 67 TRP 0.002 0.001 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (14496) covalent geometry : angle 0.63785 / 0.36 (20836) hydrogen bonds : bond 0.04248 / 2.83 ( 842) hydrogen bonds : angle 3.24803 / 2.29 ( 2147) Misc. bond : bond 0.00039 / 0.03 ( 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 201 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8917 (mtpt) REVERT: C 73 ASN cc_start: 0.8611 (t0) cc_final: 0.8167 (t0) REVERT: E 120 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8560 (mtt) REVERT: E 133 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: G 95 LYS cc_start: 0.9376 (ttmt) cc_final: 0.9132 (tmtt) REVERT: L 397 MET cc_start: 0.8218 (tpp) cc_final: 0.6508 (mtp) REVERT: L 400 GLU cc_start: 0.8615 (tt0) cc_final: 0.8165 (tm-30) REVERT: L 489 THR cc_start: 0.8614 (p) cc_final: 0.8102 (p) REVERT: L 493 HIS cc_start: 0.7566 (m90) cc_final: 0.7253 (m-70) REVERT: L 586 TRP cc_start: 0.8523 (m-10) cc_final: 0.8018 (m-10) REVERT: L 587 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8239 (tm) outliers start: 18 outliers final: 4 residues processed: 191 average time/residue: 0.9037 time to fit residues: 183.4395 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS 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 437 SER Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.101040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066669 restraints weight = 30832.095| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.56 r_work: 0.2789 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14497 Z= 0.142 Angle : 0.631 9.053 20836 Z= 0.361 Chirality : 0.043 0.206 2360 Planarity : 0.005 0.060 1617 Dihedral : 30.555 144.384 4274 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.37 % Allowed : 18.39 % Favored : 80.25 % 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: 2.14 (0.28), residues: 938 helix: 2.68 (0.21), residues: 592 sheet: -0.52 (0.67), residues: 54 loop : -0.94 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 561 TYR 0.020 0.001 TYR L 422 PHE 0.008 0.001 PHE A 67 TRP 0.002 0.001 TRP L 586 HIS 0.006 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (14496) covalent geometry : angle 0.63080 / 0.36 (20836) hydrogen bonds : bond 0.03876 / 2.59 ( 842) hydrogen bonds : angle 3.20752 / 2.26 ( 2147) Misc. bond : bond 0.00014 / 0.01 ( 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 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8916 (mtpt) REVERT: C 72 ASP cc_start: 0.8233 (m-30) cc_final: 0.8004 (m-30) REVERT: C 73 ASN cc_start: 0.8593 (t0) cc_final: 0.8139 (t0) REVERT: D 106 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (mp) REVERT: E 133 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: G 35 ARG cc_start: 0.9094 (mtm110) cc_final: 0.8807 (mtm110) REVERT: G 76 THR cc_start: 0.9248 (p) cc_final: 0.8946 (t) REVERT: G 95 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9127 (tmtt) REVERT: L 397 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.6617 (mtp) REVERT: L 400 GLU cc_start: 0.8634 (tt0) cc_final: 0.8199 (tm-30) REVERT: L 416 MET cc_start: 0.2372 (mtt) cc_final: 0.2149 (mtt) REVERT: L 479 ASN cc_start: 0.8894 (m-40) cc_final: 0.8603 (m110) REVERT: L 493 HIS cc_start: 0.7555 (m90) cc_final: 0.7337 (m-70) REVERT: L 586 TRP cc_start: 0.8486 (m-10) cc_final: 0.7917 (m-10) REVERT: L 587 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8199 (tm) outliers start: 11 outliers final: 4 residues processed: 187 average time/residue: 0.8789 time to fit residues: 174.6897 Evaluate side-chains 190 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS 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 397 MET Chi-restraints excluded: chain L residue 437 SER Chi-restraints excluded: chain L residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** 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 = 0.101366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067034 restraints weight = 30701.726| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.56 r_work: 0.2801 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14497 Z= 0.136 Angle : 0.630 10.663 20836 Z= 0.360 Chirality : 0.042 0.206 2360 Planarity : 0.004 0.045 1617 Dihedral : 30.531 144.260 4274 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.49 % Allowed : 18.26 % Favored : 80.25 % 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: 2.17 (0.28), residues: 938 helix: 2.72 (0.21), residues: 592 sheet: -0.81 (0.67), residues: 55 loop : -0.88 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE L 506 TRP 0.002 0.001 TRP L 586 HIS 0.004 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (14496) covalent geometry : angle 0.62968 / 0.36 (20836) hydrogen bonds : bond 0.03771 / 2.51 ( 842) hydrogen bonds : angle 3.18731 / 2.24 ( 2147) Misc. bond : bond 0.00011 / 0.01 ( 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 195 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8886 (mtpt) REVERT: C 73 ASN cc_start: 0.8586 (t0) cc_final: 0.8130 (t0) REVERT: D 106 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8915 (mp) REVERT: E 120 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: E 133 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: G 35 ARG cc_start: 0.9080 (mtm110) cc_final: 0.8788 (mtm110) REVERT: G 76 THR cc_start: 0.9250 (p) cc_final: 0.8953 (t) REVERT: G 95 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9113 (tmtt) REVERT: L 397 MET cc_start: 0.8298 (tpp) cc_final: 0.6596 (mtp) REVERT: L 400 GLU cc_start: 0.8632 (tt0) cc_final: 0.8326 (tm-30) REVERT: L 479 ASN cc_start: 0.8883 (m-40) cc_final: 0.8625 (m110) REVERT: L 493 HIS cc_start: 0.7516 (m90) cc_final: 0.7297 (m-70) REVERT: L 586 TRP cc_start: 0.8491 (m-10) cc_final: 0.7911 (m-10) REVERT: L 587 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (mm) outliers start: 12 outliers final: 4 residues processed: 188 average time/residue: 0.8111 time to fit residues: 162.1541 Evaluate side-chains 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS 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 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.101162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066822 restraints weight = 30854.163| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.56 r_work: 0.2793 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14497 Z= 0.153 Angle : 0.628 10.554 20836 Z= 0.359 Chirality : 0.042 0.205 2360 Planarity : 0.005 0.059 1617 Dihedral : 30.536 144.300 4274 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.37 % Allowed : 18.63 % Favored : 80.00 % 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: 2.21 (0.28), residues: 938 helix: 2.73 (0.21), residues: 593 sheet: -0.85 (0.66), residues: 55 loop : -0.83 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 561 TYR 0.009 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 TRP 0.002 0.000 TRP L 586 HIS 0.003 0.001 HIS L 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14496) covalent geometry : angle 0.62774 / 0.36 (20836) hydrogen bonds : bond 0.03851 / 2.57 ( 842) hydrogen bonds : angle 3.19747 / 2.25 ( 2147) Misc. bond : bond 0.00004 / 0.00 ( 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: 11 poor density : 182 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8882 (mtpt) REVERT: C 73 ASN cc_start: 0.8599 (t0) cc_final: 0.8145 (t0) REVERT: D 106 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8920 (mp) REVERT: E 120 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8516 (mtt) REVERT: E 133 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: G 76 THR cc_start: 0.9250 (p) cc_final: 0.8950 (t) REVERT: G 95 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9113 (tmtt) REVERT: L 397 MET cc_start: 0.8283 (tpp) cc_final: 0.6602 (mtp) REVERT: L 400 GLU cc_start: 0.8629 (tt0) cc_final: 0.8315 (tm-30) REVERT: L 479 ASN cc_start: 0.8874 (m-40) cc_final: 0.8645 (m110) REVERT: L 493 HIS cc_start: 0.7497 (m90) cc_final: 0.7284 (m-70) REVERT: L 586 TRP cc_start: 0.8518 (m-10) cc_final: 0.7943 (m-10) REVERT: L 587 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8611 (mm) outliers start: 11 outliers final: 3 residues processed: 187 average time/residue: 0.8323 time to fit residues: 165.6016 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 77 LYS 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 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 94 optimal weight: 10.9990 chunk 76 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066346 restraints weight = 30839.611| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.56 r_work: 0.2788 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14497 Z= 0.156 Angle : 0.639 10.901 20836 Z= 0.363 Chirality : 0.042 0.207 2360 Planarity : 0.005 0.046 1617 Dihedral : 30.575 144.201 4274 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 2.20 (0.28), residues: 938 helix: 2.75 (0.21), residues: 593 sheet: -1.39 (0.63), residues: 66 loop : -0.74 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 561 TYR 0.012 0.001 TYR L 407 PHE 0.008 0.001 PHE A 67 TRP 0.001 0.000 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (14496) covalent geometry : angle 0.63878 / 0.36 (20836) hydrogen bonds : bond 0.03885 / 2.59 ( 842) hydrogen bonds : angle 3.21334 / 2.26 ( 2147) Misc. bond : bond 0.00010 / 0.01 ( 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 196 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8274 (m-30) cc_final: 0.8047 (m-30) REVERT: C 73 ASN cc_start: 0.8619 (t0) cc_final: 0.8163 (t0) REVERT: D 106 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8923 (mp) REVERT: E 120 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8517 (mtt) REVERT: E 133 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: G 76 THR cc_start: 0.9246 (p) cc_final: 0.8944 (t) REVERT: G 95 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9109 (tmtt) REVERT: L 397 MET cc_start: 0.8219 (tpp) cc_final: 0.6491 (mtp) REVERT: L 400 GLU cc_start: 0.8595 (tt0) cc_final: 0.8279 (tm-30) REVERT: L 493 HIS cc_start: 0.7475 (m90) cc_final: 0.7261 (m-70) REVERT: L 586 TRP cc_start: 0.8535 (m-10) cc_final: 0.8007 (m-10) REVERT: L 587 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8610 (mm) outliers start: 12 outliers final: 4 residues processed: 189 average time/residue: 0.8930 time to fit residues: 179.3460 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER 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 587 LEU 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: 2.9990 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 110 ASN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.101009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066496 restraints weight = 30878.957| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.58 r_work: 0.2789 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14497 Z= 0.155 Angle : 0.640 11.959 20836 Z= 0.362 Chirality : 0.042 0.208 2360 Planarity : 0.005 0.047 1617 Dihedral : 30.575 144.126 4274 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.12 % Allowed : 19.50 % Favored : 79.38 % 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: 2.23 (0.28), residues: 938 helix: 2.79 (0.21), residues: 592 sheet: -1.38 (0.63), residues: 66 loop : -0.76 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 561 TYR 0.009 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 TRP 0.001 0.000 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (14496) covalent geometry : angle 0.64032 / 0.36 (20836) hydrogen bonds : bond 0.03856 / 2.57 ( 842) hydrogen bonds : angle 3.20218 / 2.25 ( 2147) Misc. bond : bond 0.00009 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5958.14 seconds wall clock time: 101 minutes 54.93 seconds (6114.93 seconds total)