Starting phenix.real_space_refine on Sun Apr 5 21:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yi_75530/04_2026/10yi_75530.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yi_75530/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/10yi_75530/04_2026/10yi_75530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yi_75530/04_2026/10yi_75530.map" model { file = "/net/cci-nas-00/data/ceres_data/10yi_75530/04_2026/10yi_75530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yi_75530/04_2026/10yi_75530.cif" } 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-2.1rc1-6017/lib/python3.9/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: 2.35, 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: 0.80 Conformation dependent library (CDL) restraints added in 335.0 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: 1.89 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: 2.53 Time building geometry restraints manager: 1.14 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=" N ILE L 420 " pdb=" CA ILE L 420 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.56e+00 bond pdb=" CA PRO G 26 " pdb=" C PRO G 26 " ideal model delta sigma weight residual 1.521 1.545 -0.024 9.30e-03 1.16e+04 6.76e+00 bond pdb=" CA GLU L 580 " pdb=" C GLU L 580 " ideal model delta sigma weight residual 1.520 1.502 0.018 1.02e-02 9.61e+03 3.09e+00 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 20424 1.84 - 3.69: 388 3.69 - 5.53: 15 5.53 - 7.38: 7 7.38 - 9.22: 2 Bond angle restraints: 20836 Sorted by residual: angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 113.18 120.55 -7.37 2.37e+00 1.78e-01 9.67e+00 angle pdb=" C1' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " ideal model delta sigma weight residual 111.00 101.78 9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " pdb=" C4' AMP L1001 " ideal model delta sigma weight residual 111.00 102.54 8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.44 -6.26 2.37e+00 1.78e-01 6.97e+00 angle pdb=" N GLN L 499 " pdb=" CA GLN L 499 " pdb=" CB GLN L 499 " ideal model delta sigma weight residual 113.65 109.99 3.66 1.47e+00 4.63e-01 6.19e+00 ... (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: 1906 0.046 - 0.092: 388 0.092 - 0.138: 63 0.138 - 0.184: 1 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: 0.000 Normalize map: mean=0, sd=1: 5.830 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.004 0.037 14497 Z= 0.196 Angle : 0.588 9.223 20836 Z= 0.350 Chirality : 0.037 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 covalent geometry : bond 0.00387 (14496) covalent geometry : angle 0.58754 (20836) hydrogen bonds : bond 0.13918 ( 842) hydrogen bonds : angle 4.68286 ( 2147) Misc. bond : bond 0.00047 ( 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 : 0.337 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: 0.8946 time to fit residues: 227.0521 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 : 0.414 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN B 93 GLN F 93 GLN G 110 ASN H 63 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.102577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068312 restraints weight = 31354.969| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.62 r_work: 0.2848 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14497 Z= 0.149 Angle : 0.563 8.531 20836 Z= 0.333 Chirality : 0.034 0.143 2360 Planarity : 0.005 0.053 1617 Dihedral : 29.893 143.842 4276 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.99 % Allowed : 14.04 % Favored : 83.98 % 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: 1.52 (0.27), residues: 938 helix: 2.01 (0.20), residues: 592 sheet: -0.20 (0.71), residues: 52 loop : -0.86 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.012 0.001 TYR L 457 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP L 586 HIS 0.007 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00321 (14496) covalent geometry : angle 0.56345 (20836) hydrogen bonds : bond 0.03531 ( 842) hydrogen bonds : angle 3.18145 ( 2147) Misc. bond : bond 0.00011 ( 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 219 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8393 (m-30) cc_final: 0.8147 (m-30) REVERT: C 73 ASN cc_start: 0.8662 (t0) cc_final: 0.8273 (t0) REVERT: D 42 TYR cc_start: 0.8677 (t80) cc_final: 0.8384 (t80) REVERT: D 106 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8893 (mp) REVERT: E 120 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8549 (mtt) REVERT: E 133 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: G 76 THR cc_start: 0.9250 (p) cc_final: 0.8925 (t) REVERT: G 92 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8829 (mm-30) REVERT: G 95 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9115 (tmtt) REVERT: L 422 TYR cc_start: 0.8939 (m-10) cc_final: 0.8615 (m-10) REVERT: L 489 THR cc_start: 0.8618 (p) cc_final: 0.8069 (p) REVERT: L 493 HIS cc_start: 0.7581 (m90) cc_final: 0.7308 (m-70) REVERT: L 561 ARG cc_start: 0.8972 (tmt-80) cc_final: 0.8584 (tmm160) outliers start: 16 outliers final: 5 residues processed: 210 average time/residue: 0.8658 time to fit residues: 192.7858 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 SER 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: 4.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.102453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068194 restraints weight = 31233.793| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.58 r_work: 0.2820 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14497 Z= 0.151 Angle : 0.567 7.631 20836 Z= 0.333 Chirality : 0.034 0.142 2360 Planarity : 0.004 0.043 1617 Dihedral : 29.923 143.543 4276 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.37 % Allowed : 15.90 % 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: 2.06 (0.27), residues: 938 helix: 2.55 (0.21), residues: 592 sheet: -0.76 (0.62), residues: 62 loop : -0.76 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 426 TYR 0.013 0.001 TYR L 457 PHE 0.010 0.001 PHE L 543 TRP 0.002 0.001 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00328 (14496) covalent geometry : angle 0.56745 (20836) hydrogen bonds : bond 0.03309 ( 842) hydrogen bonds : angle 3.04308 ( 2147) Misc. bond : bond 0.00021 ( 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 206 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8384 (m-30) cc_final: 0.8125 (m-30) REVERT: C 73 ASN cc_start: 0.8613 (t0) cc_final: 0.8192 (t0) REVERT: D 42 TYR cc_start: 0.8628 (t80) cc_final: 0.8334 (t80) REVERT: E 133 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: G 35 ARG cc_start: 0.9115 (mtm110) cc_final: 0.8817 (mtm110) REVERT: G 76 THR cc_start: 0.9249 (p) cc_final: 0.8946 (t) REVERT: G 92 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8826 (mm-30) REVERT: G 95 LYS cc_start: 0.9389 (ttmt) cc_final: 0.9133 (tmtt) REVERT: L 422 TYR cc_start: 0.8843 (m-10) cc_final: 0.8396 (m-10) REVERT: L 479 ASN cc_start: 0.8826 (m-40) cc_final: 0.8490 (m110) REVERT: L 493 HIS cc_start: 0.7449 (m90) cc_final: 0.7246 (m-70) REVERT: L 534 MET cc_start: 0.7827 (ttp) cc_final: 0.7621 (ttp) outliers start: 11 outliers final: 5 residues processed: 201 average time/residue: 0.8660 time to fit residues: 184.6498 Evaluate side-chains 186 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain G residue 107 VAL 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: 5.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 110 ASN L 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068309 restraints weight = 30958.709| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.57 r_work: 0.2822 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14497 Z= 0.151 Angle : 0.568 8.416 20836 Z= 0.330 Chirality : 0.034 0.144 2360 Planarity : 0.004 0.042 1617 Dihedral : 29.906 142.955 4276 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 18.01 % Favored : 80.12 % 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: 2.31 (0.28), residues: 938 helix: 2.76 (0.21), residues: 593 sheet: -0.54 (0.67), residues: 55 loop : -0.75 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 527 TYR 0.010 0.001 TYR L 579 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.002 TRP L 586 HIS 0.004 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00330 (14496) covalent geometry : angle 0.56795 (20836) hydrogen bonds : bond 0.03283 ( 842) hydrogen bonds : angle 3.02924 ( 2147) Misc. bond : bond 0.00002 ( 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 206 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8369 (m-30) cc_final: 0.8123 (m-30) REVERT: C 73 ASN cc_start: 0.8624 (t0) cc_final: 0.8177 (t0) REVERT: D 42 TYR cc_start: 0.8655 (t80) cc_final: 0.8355 (t80) REVERT: D 63 ASN cc_start: 0.9017 (m-40) cc_final: 0.8677 (m110) REVERT: E 120 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: E 133 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: F 93 GLN cc_start: 0.8516 (mt0) cc_final: 0.8280 (mp10) REVERT: G 76 THR cc_start: 0.9250 (p) cc_final: 0.8959 (t) REVERT: G 95 LYS cc_start: 0.9383 (ttmt) cc_final: 0.9121 (tmtt) REVERT: L 397 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6915 (mtp) REVERT: L 466 HIS cc_start: 0.8514 (p-80) cc_final: 0.8282 (p-80) REVERT: L 546 MET cc_start: 0.8659 (pmm) cc_final: 0.8288 (pmm) REVERT: L 586 TRP cc_start: 0.8322 (m-10) cc_final: 0.7671 (m-10) outliers start: 15 outliers final: 7 residues processed: 201 average time/residue: 0.8085 time to fit residues: 172.7670 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 : 0.380 ------------------------------------------------------------------------------- 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 397 MET 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: 1.9990 chunk 112 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN F 93 GLN G 110 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.103360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068837 restraints weight = 31257.800| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.63 r_work: 0.2834 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14497 Z= 0.142 Angle : 0.560 8.804 20836 Z= 0.327 Chirality : 0.034 0.142 2360 Planarity : 0.004 0.041 1617 Dihedral : 29.852 142.684 4276 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.49 % Allowed : 18.76 % Favored : 79.75 % 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: 2.46 (0.28), residues: 938 helix: 2.91 (0.21), residues: 593 sheet: -0.64 (0.69), residues: 55 loop : -0.73 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.015 0.001 TYR L 422 PHE 0.007 0.001 PHE A 67 TRP 0.002 0.001 TRP L 586 HIS 0.002 0.000 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00306 (14496) covalent geometry : angle 0.55996 (20836) hydrogen bonds : bond 0.03179 ( 842) hydrogen bonds : angle 2.96753 ( 2147) Misc. bond : bond 0.00007 ( 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 203 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8339 (m-30) cc_final: 0.8091 (m-30) REVERT: C 73 ASN cc_start: 0.8609 (t0) cc_final: 0.8151 (t0) REVERT: D 42 TYR cc_start: 0.8620 (t80) cc_final: 0.8324 (t80) REVERT: D 63 ASN cc_start: 0.9014 (m-40) cc_final: 0.8645 (m110) REVERT: D 68 ASP cc_start: 0.9103 (t0) cc_final: 0.8826 (t0) REVERT: E 120 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: E 133 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: G 76 THR cc_start: 0.9227 (p) cc_final: 0.8948 (t) REVERT: G 95 LYS cc_start: 0.9405 (ttmt) cc_final: 0.9095 (tmtt) REVERT: L 466 HIS cc_start: 0.8635 (p-80) cc_final: 0.8404 (p-80) REVERT: L 489 THR cc_start: 0.8583 (p) cc_final: 0.8264 (p) REVERT: L 586 TRP cc_start: 0.8189 (m-10) cc_final: 0.7578 (m-10) outliers start: 12 outliers final: 3 residues processed: 195 average time/residue: 0.8424 time to fit residues: 174.3096 Evaluate side-chains 188 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain L residue 437 SER 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: 4.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065279 restraints weight = 31115.202| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.64 r_work: 0.2763 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14497 Z= 0.226 Angle : 0.598 8.118 20836 Z= 0.346 Chirality : 0.036 0.150 2360 Planarity : 0.004 0.045 1617 Dihedral : 30.102 145.167 4274 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 19.13 % Favored : 79.13 % 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: 2.24 (0.28), residues: 938 helix: 2.76 (0.21), residues: 593 sheet: -0.88 (0.64), residues: 61 loop : -0.80 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.011 0.001 TYR L 422 PHE 0.009 0.001 PHE A 67 TRP 0.004 0.001 TRP L 586 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00513 (14496) covalent geometry : angle 0.59824 (20836) hydrogen bonds : bond 0.03854 ( 842) hydrogen bonds : angle 3.16136 ( 2147) Misc. bond : bond 0.00011 ( 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 200 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8388 (m-30) cc_final: 0.8136 (m-30) REVERT: C 73 ASN cc_start: 0.8624 (t0) cc_final: 0.8176 (t0) REVERT: D 42 TYR cc_start: 0.8733 (t80) cc_final: 0.8454 (t80) REVERT: D 106 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8972 (mp) REVERT: E 120 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8551 (mtt) REVERT: E 133 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: G 95 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9102 (tmtt) REVERT: L 397 MET cc_start: 0.8281 (mtp) cc_final: 0.6658 (mtm) REVERT: L 409 MET cc_start: 0.8681 (tpt) cc_final: 0.8399 (mmm) REVERT: L 466 HIS cc_start: 0.8727 (p-80) cc_final: 0.8512 (p-80) REVERT: L 489 THR cc_start: 0.8660 (p) cc_final: 0.8315 (p) outliers start: 14 outliers final: 5 residues processed: 195 average time/residue: 0.8134 time to fit residues: 168.7278 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 : 0.368 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.102192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067488 restraints weight = 31141.920| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.62 r_work: 0.2828 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2496 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= 0.152 Angle : 0.584 8.768 20836 Z= 0.338 Chirality : 0.034 0.141 2360 Planarity : 0.004 0.048 1617 Dihedral : 29.885 142.953 4274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.74 % Allowed : 19.01 % 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: 2.44 (0.28), residues: 938 helix: 2.87 (0.21), residues: 594 sheet: -0.09 (0.71), residues: 54 loop : -0.79 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.009 0.001 TYR H 40 PHE 0.009 0.001 PHE A 67 TRP 0.046 0.015 TRP L 586 HIS 0.002 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00333 (14496) covalent geometry : angle 0.58385 (20836) hydrogen bonds : bond 0.03285 ( 842) hydrogen bonds : angle 3.06004 ( 2147) Misc. bond : bond 0.00007 ( 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 201 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8377 (m-30) cc_final: 0.8123 (m-30) REVERT: C 73 ASN cc_start: 0.8649 (t0) cc_final: 0.8200 (t0) REVERT: D 42 TYR cc_start: 0.8685 (t80) cc_final: 0.8411 (t80) REVERT: D 63 ASN cc_start: 0.9029 (m-40) cc_final: 0.8694 (m110) REVERT: D 68 ASP cc_start: 0.9116 (t0) cc_final: 0.8830 (t0) REVERT: D 106 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8920 (mp) REVERT: E 120 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: E 133 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: G 76 THR cc_start: 0.9246 (p) cc_final: 0.8940 (t) REVERT: G 95 LYS cc_start: 0.9393 (ttmt) cc_final: 0.9109 (tmtt) outliers start: 14 outliers final: 3 residues processed: 195 average time/residue: 0.8150 time to fit residues: 169.0730 Evaluate side-chains 188 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 G residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN L 493 HIS L 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067967 restraints weight = 31019.380| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.58 r_work: 0.2813 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14497 Z= 0.154 Angle : 0.591 9.280 20836 Z= 0.341 Chirality : 0.034 0.144 2360 Planarity : 0.004 0.043 1617 Dihedral : 29.837 142.519 4274 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.12 % Allowed : 20.12 % Favored : 78.76 % 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: 2.47 (0.28), residues: 938 helix: 2.90 (0.21), residues: 593 sheet: -0.21 (0.75), residues: 48 loop : -0.77 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.022 0.001 TYR L 579 PHE 0.008 0.001 PHE A 67 TRP 0.030 0.007 TRP L 586 HIS 0.003 0.001 HIS L 466 Details of bonding type rmsd covalent geometry : bond 0.00340 (14496) covalent geometry : angle 0.59136 (20836) hydrogen bonds : bond 0.03258 ( 842) hydrogen bonds : angle 3.06743 ( 2147) Misc. bond : bond 0.00004 ( 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 197 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8347 (m-30) cc_final: 0.8104 (m-30) REVERT: C 73 ASN cc_start: 0.8641 (t0) cc_final: 0.8177 (t0) REVERT: D 42 TYR cc_start: 0.8683 (t80) cc_final: 0.8418 (t80) REVERT: D 63 ASN cc_start: 0.9035 (m-40) cc_final: 0.8698 (m110) REVERT: D 68 ASP cc_start: 0.9117 (t0) cc_final: 0.8861 (t0) REVERT: D 86 ARG cc_start: 0.9023 (mmt-90) cc_final: 0.8744 (mmt90) REVERT: D 106 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8869 (mp) REVERT: E 120 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: E 133 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: G 76 THR cc_start: 0.9242 (p) cc_final: 0.8940 (t) REVERT: G 95 LYS cc_start: 0.9401 (ttmt) cc_final: 0.9106 (tmtt) REVERT: L 479 ASN cc_start: 0.8850 (m-40) cc_final: 0.8589 (m110) outliers start: 9 outliers final: 3 residues processed: 193 average time/residue: 0.8470 time to fit residues: 173.8639 Evaluate side-chains 189 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN L 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.102142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067429 restraints weight = 31162.745| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.62 r_work: 0.2824 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14497 Z= 0.168 Angle : 0.614 10.002 20836 Z= 0.349 Chirality : 0.035 0.161 2360 Planarity : 0.004 0.043 1617 Dihedral : 29.848 142.897 4274 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.37 % Allowed : 20.62 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.28), residues: 938 helix: 2.88 (0.21), residues: 593 sheet: -0.20 (0.76), residues: 48 loop : -0.83 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 42 TYR 0.009 0.001 TYR L 407 PHE 0.008 0.001 PHE A 67 TRP 0.022 0.005 TRP L 586 HIS 0.003 0.001 HIS L 466 Details of bonding type rmsd covalent geometry : bond 0.00374 (14496) covalent geometry : angle 0.61446 (20836) hydrogen bonds : bond 0.03364 ( 842) hydrogen bonds : angle 3.10291 ( 2147) Misc. bond : bond 0.00003 ( 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 : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.8092 (m-30) REVERT: C 73 ASN cc_start: 0.8655 (t0) cc_final: 0.8188 (t0) REVERT: D 42 TYR cc_start: 0.8695 (t80) cc_final: 0.8456 (t80) REVERT: D 63 ASN cc_start: 0.9039 (m-40) cc_final: 0.8688 (m110) REVERT: D 86 ARG cc_start: 0.9054 (mmt-90) cc_final: 0.8779 (mmt90) REVERT: D 106 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8907 (mp) REVERT: E 120 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8432 (mtt) REVERT: E 133 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: G 76 THR cc_start: 0.9245 (p) cc_final: 0.8943 (t) REVERT: G 95 LYS cc_start: 0.9400 (ttmt) cc_final: 0.9111 (tmtt) REVERT: L 479 ASN cc_start: 0.8808 (m-40) cc_final: 0.8550 (m110) REVERT: L 519 MET cc_start: 0.8599 (pmm) cc_final: 0.7837 (mpp) outliers start: 11 outliers final: 3 residues processed: 187 average time/residue: 0.8374 time to fit residues: 166.2951 Evaluate side-chains 183 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 G residue 107 VAL 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: 6.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN L 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.066287 restraints weight = 31119.435| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.63 r_work: 0.2783 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14497 Z= 0.191 Angle : 0.630 11.498 20836 Z= 0.356 Chirality : 0.036 0.306 2360 Planarity : 0.004 0.044 1617 Dihedral : 29.934 144.066 4274 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.37 % Allowed : 20.75 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.28), residues: 938 helix: 2.80 (0.21), residues: 591 sheet: -0.28 (0.75), residues: 48 loop : -0.88 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.014 0.001 TYR L 579 PHE 0.014 0.001 PHE L 487 TRP 0.023 0.005 TRP L 586 HIS 0.003 0.001 HIS L 466 Details of bonding type rmsd covalent geometry : bond 0.00431 (14496) covalent geometry : angle 0.62997 (20836) hydrogen bonds : bond 0.03575 ( 842) hydrogen bonds : angle 3.17865 ( 2147) Misc. bond : bond 0.00003 ( 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 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8348 (m-30) cc_final: 0.8120 (m-30) REVERT: C 73 ASN cc_start: 0.8664 (t0) cc_final: 0.8200 (t0) REVERT: D 42 TYR cc_start: 0.8730 (t80) cc_final: 0.8445 (t80) REVERT: D 86 ARG cc_start: 0.9068 (mmt-90) cc_final: 0.8793 (mmt90) REVERT: D 106 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8918 (mp) REVERT: E 120 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8516 (mtt) REVERT: E 133 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: G 95 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9114 (tmtt) REVERT: L 479 ASN cc_start: 0.8850 (m-40) cc_final: 0.8582 (m110) outliers start: 11 outliers final: 5 residues processed: 186 average time/residue: 0.8356 time to fit residues: 165.1320 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 : 0.329 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN L 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.101801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066921 restraints weight = 31221.146| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.63 r_work: 0.2798 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14497 Z= 0.174 Angle : 0.628 11.911 20836 Z= 0.355 Chirality : 0.036 0.267 2360 Planarity : 0.004 0.043 1617 Dihedral : 29.904 143.638 4274 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.24 % Allowed : 21.12 % Favored : 77.64 % 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: 2.29 (0.28), residues: 938 helix: 2.79 (0.21), residues: 592 sheet: -0.35 (0.75), residues: 48 loop : -0.87 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.016 0.001 TYR L 407 PHE 0.010 0.001 PHE L 487 TRP 0.021 0.005 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00389 (14496) covalent geometry : angle 0.62766 (20836) hydrogen bonds : bond 0.03468 ( 842) hydrogen bonds : angle 3.16470 ( 2147) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5569.08 seconds wall clock time: 94 minutes 59.67 seconds (5699.67 seconds total)