Starting phenix.real_space_refine on Sun Apr 5 21:57:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yh_75529/04_2026/10yh_75529.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yh_75529/04_2026/10yh_75529.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/10yh_75529/04_2026/10yh_75529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yh_75529/04_2026/10yh_75529.map" model { file = "/net/cci-nas-00/data/ceres_data/10yh_75529/04_2026/10yh_75529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yh_75529/04_2026/10yh_75529.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= 0.004 sd= 1.021 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 2 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: 2.57, per 1000 atoms: 0.19 Number of scatterers: 13642 At special positions: 0 Unit cell: (88.02, 123.88, 137.572, 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: 1.12 Conformation dependent library (CDL) restraints added in 482.2 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: 42 helices and 11 sheets defined 63.0% alpha, 10.4% beta 147 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.510A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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 76 removed outlier: 3.735A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.545A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.410A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.622A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.557A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.043A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.304A 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 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 76 removed outlier: 3.852A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.328A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 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 452 Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 486 through 490 removed outlier: 3.536A pdb=" N THR L 489 " --> pdb=" O PRO L 486 " (cutoff:3.500A) removed outlier: 3.815A 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: 4.317A pdb=" N MET L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 3.757A 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: 7.210A 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: 6.484A 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: 7.414A 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 'E' and resid 83 through 84 removed outlier: 7.199A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.389A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 398 through 401 removed outlier: 6.519A pdb=" N LEU L 398 " --> pdb=" O ARG L 584 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N HIS L 585 " --> pdb=" O ASP L 574 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP L 574 " --> pdb=" O HIS L 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 436 through 439 removed outlier: 7.206A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 483 through 485 removed outlier: 3.780A pdb=" N LYS L 483 " --> pdb=" O ASP L 478 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU L 476 " --> pdb=" O LEU L 485 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET L 542 " --> pdb=" O VAL L 507 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASP L 509 " --> pdb=" O MET L 542 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2005 1.32 - 1.45: 4992 1.45 - 1.57: 6868 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14496 Sorted by residual: bond pdb=" N ILE L 420 " pdb=" CA ILE L 420 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.22e-02 6.72e+03 7.68e+00 bond pdb=" N LYS L 421 " pdb=" CA LYS L 421 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.27e-02 6.20e+03 3.04e+00 bond pdb=" CA LEU L 485 " pdb=" C LEU L 485 " ideal model delta sigma weight residual 1.519 1.504 0.015 9.50e-03 1.11e+04 2.52e+00 bond pdb=" C3' DC K 126 " pdb=" O3' DC K 126 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" C4' AMP L1001 " pdb=" O4' AMP L1001 " ideal model delta sigma weight residual 1.426 1.453 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 20353 1.84 - 3.67: 464 3.67 - 5.51: 9 5.51 - 7.34: 8 7.34 - 9.18: 2 Bond angle restraints: 20836 Sorted by residual: angle pdb=" C1' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " ideal model delta sigma weight residual 111.00 101.82 9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " pdb=" C4' AMP L1001 " ideal model delta sigma weight residual 111.00 102.68 8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.38 -6.20 2.37e+00 1.78e-01 6.83e+00 angle pdb=" CA ILE L 420 " pdb=" C ILE L 420 " pdb=" O ILE L 420 " ideal model delta sigma weight residual 121.23 118.45 2.78 1.07e+00 8.73e-01 6.77e+00 angle pdb=" O ILE L 420 " pdb=" C ILE L 420 " pdb=" N LYS L 421 " ideal model delta sigma weight residual 122.61 125.40 -2.79 1.09e+00 8.42e-01 6.57e+00 ... (remaining 20831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 6174 28.69 - 57.38: 1640 57.38 - 86.08: 145 86.08 - 114.77: 1 114.77 - 143.46: 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 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+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 76.54 143.46 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC K 126 " pdb=" C3' DC K 126 " pdb=" O3' DC K 126 " pdb=" P DC K 127 " ideal model delta sinusoidal sigma weight residual 220.00 77.79 142.21 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 7959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1777 0.047 - 0.093: 504 0.093 - 0.140: 75 0.140 - 0.186: 2 0.186 - 0.233: 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 1.36e+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 -0.20 2.00e-01 2.50e+01 9.68e-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 7.39e-01 ... (remaining 2357 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 43 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 580 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO L 581 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 581 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 581 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 61 " 0.026 2.00e-02 2.50e+03 1.14e-02 3.58e+00 pdb=" N9 DA I 61 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 61 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 61 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 61 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 61 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 61 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 61 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 61 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 61 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 61 " -0.004 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5986 2.98 - 3.46: 12725 3.46 - 3.94: 27428 3.94 - 4.42: 30729 4.42 - 4.90: 41580 Nonbonded interactions: 118448 Sorted by model distance: nonbonded pdb=" O5' DG K 95 " pdb=" O4' DG K 95 " model vdw 2.496 2.432 nonbonded pdb=" N1 DG K 94 " pdb=" C4 DG K 94 " model vdw 2.573 2.672 nonbonded pdb=" N1 DG I 100 " pdb=" C4 DG I 100 " model vdw 2.574 2.672 nonbonded pdb=" N1 DG I 63 " pdb=" C4 DG I 63 " model vdw 2.574 2.672 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.574 2.672 ... (remaining 118443 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: 5.690 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.008 0.058 14497 Z= 0.351 Angle : 0.629 9.176 20836 Z= 0.368 Chirality : 0.042 0.233 2360 Planarity : 0.005 0.056 1617 Dihedral : 26.462 143.461 6174 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.25 % Allowed : 4.60 % Favored : 95.16 % 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: 0.98 (0.27), residues: 938 helix: 1.65 (0.21), residues: 588 sheet: 0.29 (0.85), residues: 44 loop : -1.30 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 45 TYR 0.012 0.002 TYR L 512 PHE 0.013 0.002 PHE L 454 TRP 0.002 0.001 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00811 (14496) covalent geometry : angle 0.62941 (20836) hydrogen bonds : bond 0.12039 ( 838) hydrogen bonds : angle 4.24747 ( 2129) Misc. bond : bond 0.00012 ( 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 254 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.257 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: B 35 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8006 (mtt180) REVERT: C 24 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8926 (mm-40) REVERT: C 64 GLU cc_start: 0.8556 (tt0) cc_final: 0.8302 (tp30) REVERT: C 110 ASN cc_start: 0.8752 (t0) cc_final: 0.8377 (p0) REVERT: E 64 LYS cc_start: 0.8958 (mttt) cc_final: 0.8631 (mtmm) REVERT: F 79 LYS cc_start: 0.8684 (mttm) cc_final: 0.8238 (mtpt) REVERT: G 35 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8703 (mtt90) REVERT: G 64 GLU cc_start: 0.8548 (tt0) cc_final: 0.8277 (tp30) REVERT: H 35 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7504 (mm-30) REVERT: L 422 TYR cc_start: 0.6921 (m-80) cc_final: 0.6587 (m-80) REVERT: L 534 MET cc_start: 0.6328 (ttt) cc_final: 0.5905 (tmm) REVERT: L 537 ILE cc_start: 0.8414 (pt) cc_final: 0.8163 (mp) REVERT: L 541 ILE cc_start: 0.8817 (mp) cc_final: 0.8069 (pp) REVERT: L 545 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8436 (pt0) outliers start: 2 outliers final: 1 residues processed: 253 average time/residue: 0.9424 time to fit residues: 252.3123 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 485 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN E 68 GLN G 73 ASN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067885 restraints weight = 28939.986| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.45 r_work: 0.2762 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14497 Z= 0.166 Angle : 0.569 7.486 20836 Z= 0.337 Chirality : 0.035 0.161 2360 Planarity : 0.004 0.051 1617 Dihedral : 30.135 143.019 4276 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.60 % Allowed : 14.53 % Favored : 81.86 % 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: 1.69 (0.28), residues: 938 helix: 2.19 (0.21), residues: 596 sheet: 0.18 (0.79), residues: 48 loop : -1.01 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 561 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE L 454 TRP 0.003 0.001 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00365 (14496) covalent geometry : angle 0.56870 (20836) hydrogen bonds : bond 0.03844 ( 838) hydrogen bonds : angle 3.20445 ( 2129) Misc. bond : bond 0.00116 ( 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 221 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9246 (t0) cc_final: 0.8870 (t0) REVERT: C 110 ASN cc_start: 0.8900 (t0) cc_final: 0.8590 (p0) REVERT: E 64 LYS cc_start: 0.9178 (mttt) cc_final: 0.8952 (mtmm) REVERT: F 79 LYS cc_start: 0.9094 (mttm) cc_final: 0.8804 (mtpt) REVERT: G 56 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8906 (tt0) REVERT: H 35 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7826 (mm-30) REVERT: L 397 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6619 (tpt) REVERT: L 475 LEU cc_start: 0.8158 (mm) cc_final: 0.7946 (mm) REVERT: L 507 VAL cc_start: 0.7206 (OUTLIER) cc_final: 0.6813 (p) REVERT: L 534 MET cc_start: 0.6488 (ttt) cc_final: 0.5969 (tmm) REVERT: L 541 ILE cc_start: 0.8634 (mp) cc_final: 0.8421 (pp) REVERT: L 583 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6440 (pttm) REVERT: L 586 TRP cc_start: 0.7645 (m100) cc_final: 0.6869 (m100) outliers start: 29 outliers final: 2 residues processed: 205 average time/residue: 0.9428 time to fit residues: 204.7875 Evaluate side-chains 180 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 430 HIS Chi-restraints excluded: chain L residue 507 VAL Chi-restraints excluded: chain L residue 583 LYS 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: 0.7980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 95 GLN F 93 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** 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 = 0.3686 r_free = 0.3686 target = 0.104010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067485 restraints weight = 29046.315| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.45 r_work: 0.2747 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14497 Z= 0.159 Angle : 0.550 6.309 20836 Z= 0.327 Chirality : 0.035 0.146 2360 Planarity : 0.004 0.047 1617 Dihedral : 30.058 142.096 4274 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.11 % Allowed : 16.89 % 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: 1.97 (0.28), residues: 938 helix: 2.42 (0.21), residues: 596 sheet: 0.41 (0.77), residues: 48 loop : -0.95 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.010 0.001 TYR L 593 PHE 0.009 0.001 PHE L 454 TRP 0.009 0.002 TRP L 586 HIS 0.010 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00347 (14496) covalent geometry : angle 0.55034 (20836) hydrogen bonds : bond 0.03419 ( 838) hydrogen bonds : angle 3.04877 ( 2129) Misc. bond : bond 0.00002 ( 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 204 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: C 73 ASN cc_start: 0.9223 (t0) cc_final: 0.8820 (t0) REVERT: D 108 LYS cc_start: 0.8767 (pttp) cc_final: 0.8564 (ptpp) REVERT: D 113 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: E 64 LYS cc_start: 0.9153 (mttt) cc_final: 0.8926 (mtmm) REVERT: F 79 LYS cc_start: 0.9108 (mttm) cc_final: 0.8835 (mtpt) REVERT: H 35 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7921 (mm-30) REVERT: L 397 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7273 (mmm) REVERT: L 468 MET cc_start: 0.6654 (mpt) cc_final: 0.6151 (mmp) REVERT: L 534 MET cc_start: 0.6935 (ttt) cc_final: 0.6294 (tmm) outliers start: 25 outliers final: 6 residues processed: 191 average time/residue: 0.9209 time to fit residues: 186.7682 Evaluate side-chains 179 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 430 HIS Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU 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: 1.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.066297 restraints weight = 28714.201| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.44 r_work: 0.2721 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14497 Z= 0.173 Angle : 0.552 7.444 20836 Z= 0.327 Chirality : 0.035 0.155 2360 Planarity : 0.004 0.046 1617 Dihedral : 30.083 142.454 4274 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.73 % Allowed : 18.39 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.28), residues: 938 helix: 2.51 (0.21), residues: 596 sheet: 0.53 (0.77), residues: 48 loop : -1.00 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE L 454 TRP 0.004 0.001 TRP L 586 HIS 0.005 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00382 (14496) covalent geometry : angle 0.55170 (20836) hydrogen bonds : bond 0.03446 ( 838) hydrogen bonds : angle 3.00034 ( 2129) Misc. bond : bond 0.00013 ( 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 199 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9208 (t0) cc_final: 0.8792 (t0) REVERT: D 113 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: E 64 LYS cc_start: 0.9138 (mttt) cc_final: 0.8896 (mtmm) REVERT: F 79 LYS cc_start: 0.9150 (mttm) cc_final: 0.8880 (mtpt) REVERT: G 73 ASN cc_start: 0.8758 (t0) cc_final: 0.8283 (t0) REVERT: L 397 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7479 (mmm) REVERT: L 534 MET cc_start: 0.6826 (ttt) cc_final: 0.6376 (tmm) REVERT: L 585 HIS cc_start: 0.8334 (m90) cc_final: 0.8116 (m90) outliers start: 22 outliers final: 4 residues processed: 187 average time/residue: 0.8768 time to fit residues: 174.0135 Evaluate side-chains 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 535 VAL 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: 10.0000 chunk 46 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN G 104 GLN H 47 GLN ** L 502 ASN ** 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 = 0.3653 r_free = 0.3653 target = 0.102232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065588 restraints weight = 28833.821| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.44 r_work: 0.2706 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14497 Z= 0.189 Angle : 0.566 8.152 20836 Z= 0.332 Chirality : 0.035 0.144 2360 Planarity : 0.004 0.046 1617 Dihedral : 30.107 142.725 4274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.86 % Allowed : 18.76 % Favored : 78.39 % 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: 1.98 (0.28), residues: 938 helix: 2.48 (0.21), residues: 596 sheet: -0.25 (0.69), residues: 60 loop : -0.94 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE L 506 TRP 0.004 0.001 TRP L 586 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (14496) covalent geometry : angle 0.56627 (20836) hydrogen bonds : bond 0.03516 ( 838) hydrogen bonds : angle 3.00276 ( 2129) Misc. bond : bond 0.00034 ( 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 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: C 73 ASN cc_start: 0.9185 (t0) cc_final: 0.8737 (t0) REVERT: D 113 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: E 64 LYS cc_start: 0.9150 (mttt) cc_final: 0.8934 (mtmm) REVERT: F 79 LYS cc_start: 0.9177 (mttm) cc_final: 0.8914 (mtpt) REVERT: G 73 ASN cc_start: 0.8814 (t0) cc_final: 0.8311 (t0) REVERT: L 397 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7342 (mmm) REVERT: L 468 MET cc_start: 0.6720 (mpt) cc_final: 0.6186 (mmp) REVERT: L 534 MET cc_start: 0.6922 (ttt) cc_final: 0.6475 (tmm) REVERT: L 585 HIS cc_start: 0.8339 (m90) cc_final: 0.8039 (m90) outliers start: 23 outliers final: 10 residues processed: 177 average time/residue: 0.8602 time to fit residues: 162.0415 Evaluate side-chains 175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 62 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN G 104 GLN ** L 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066477 restraints weight = 28315.298| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.43 r_work: 0.2766 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14497 Z= 0.163 Angle : 0.559 8.374 20836 Z= 0.328 Chirality : 0.034 0.144 2360 Planarity : 0.004 0.045 1617 Dihedral : 30.077 142.854 4274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.86 % Allowed : 19.13 % 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: 2.02 (0.28), residues: 938 helix: 2.51 (0.21), residues: 596 sheet: -0.28 (0.70), residues: 60 loop : -0.93 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.009 0.001 TYR C 57 PHE 0.011 0.001 PHE L 506 TRP 0.006 0.002 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00359 (14496) covalent geometry : angle 0.55884 (20836) hydrogen bonds : bond 0.03336 ( 838) hydrogen bonds : angle 3.00035 ( 2129) Misc. bond : bond 0.00020 ( 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 190 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: C 73 ASN cc_start: 0.9171 (t0) cc_final: 0.8716 (t0) REVERT: D 113 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: E 64 LYS cc_start: 0.9098 (mttt) cc_final: 0.8878 (mtmm) REVERT: F 79 LYS cc_start: 0.9177 (mttm) cc_final: 0.8913 (mtpt) REVERT: G 73 ASN cc_start: 0.8830 (t0) cc_final: 0.8337 (t0) REVERT: L 397 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6833 (tpp) REVERT: L 534 MET cc_start: 0.6806 (ttt) cc_final: 0.6383 (tmm) REVERT: L 585 HIS cc_start: 0.8336 (m90) cc_final: 0.8026 (m90) outliers start: 23 outliers final: 8 residues processed: 175 average time/residue: 0.8651 time to fit residues: 160.8950 Evaluate side-chains 176 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 535 VAL 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: 0.9980 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066605 restraints weight = 28298.814| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.39 r_work: 0.2747 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14497 Z= 0.177 Angle : 0.564 10.010 20836 Z= 0.330 Chirality : 0.035 0.143 2360 Planarity : 0.004 0.046 1617 Dihedral : 30.052 142.828 4274 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.48 % Allowed : 19.63 % 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: 2.04 (0.28), residues: 938 helix: 2.53 (0.21), residues: 596 sheet: -0.20 (0.70), residues: 61 loop : -0.95 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 521 TYR 0.009 0.001 TYR C 57 PHE 0.012 0.001 PHE L 506 TRP 0.005 0.002 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (14496) covalent geometry : angle 0.56403 (20836) hydrogen bonds : bond 0.03395 ( 838) hydrogen bonds : angle 2.95169 ( 2129) Misc. bond : bond 0.00025 ( 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 189 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8959 (tt0) REVERT: C 64 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: C 73 ASN cc_start: 0.9149 (t0) cc_final: 0.8691 (t0) REVERT: D 113 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: E 64 LYS cc_start: 0.9096 (mttt) cc_final: 0.8881 (mtmm) REVERT: F 79 LYS cc_start: 0.9180 (mttm) cc_final: 0.8925 (mtpt) REVERT: G 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8361 (t0) REVERT: L 397 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6912 (tpp) REVERT: L 468 MET cc_start: 0.6702 (mpt) cc_final: 0.6114 (mmp) REVERT: L 534 MET cc_start: 0.6644 (ttt) cc_final: 0.6208 (tmm) REVERT: L 557 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8645 (p0) REVERT: L 585 HIS cc_start: 0.8384 (m90) cc_final: 0.8083 (m90) outliers start: 20 outliers final: 8 residues processed: 176 average time/residue: 0.8767 time to fit residues: 164.1321 Evaluate side-chains 179 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066648 restraints weight = 28112.387| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.40 r_work: 0.2789 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14497 Z= 0.161 Angle : 0.567 10.897 20836 Z= 0.330 Chirality : 0.035 0.145 2360 Planarity : 0.004 0.045 1617 Dihedral : 30.030 142.942 4274 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.23 % Allowed : 19.25 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.28), residues: 938 helix: 2.58 (0.21), residues: 596 sheet: -0.13 (0.70), residues: 61 loop : -0.94 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.009 0.001 TYR H 42 PHE 0.015 0.001 PHE L 506 TRP 0.007 0.002 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00355 (14496) covalent geometry : angle 0.56729 (20836) hydrogen bonds : bond 0.03306 ( 838) hydrogen bonds : angle 2.94447 ( 2129) Misc. bond : bond 0.00021 ( 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: 26 poor density : 171 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8940 (tt0) REVERT: C 64 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: C 73 ASN cc_start: 0.9141 (t0) cc_final: 0.8671 (t0) REVERT: D 113 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: E 64 LYS cc_start: 0.9068 (mttt) cc_final: 0.8854 (mtmm) REVERT: F 79 LYS cc_start: 0.9181 (mttm) cc_final: 0.8932 (mtpt) REVERT: G 73 ASN cc_start: 0.8837 (t0) cc_final: 0.8359 (t0) REVERT: H 33 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7282 (mtt180) REVERT: H 76 GLU cc_start: 0.9047 (tp30) cc_final: 0.8845 (tp30) REVERT: H 79 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8481 (mtm-85) REVERT: L 397 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: L 418 SER cc_start: 0.7585 (t) cc_final: 0.7142 (m) REVERT: L 468 MET cc_start: 0.6633 (mpt) cc_final: 0.6065 (mmp) REVERT: L 534 MET cc_start: 0.6534 (ttt) cc_final: 0.6232 (tmm) REVERT: L 557 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (p0) REVERT: L 585 HIS cc_start: 0.8410 (m90) cc_final: 0.8047 (m-70) outliers start: 26 outliers final: 10 residues processed: 180 average time/residue: 0.8900 time to fit residues: 170.3578 Evaluate side-chains 184 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 546 MET Chi-restraints excluded: chain L residue 557 ASP 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: 0.9990 chunk 112 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN L 449 HIS ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068313 restraints weight = 28460.523| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.42 r_work: 0.2802 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14497 Z= 0.142 Angle : 0.568 11.829 20836 Z= 0.330 Chirality : 0.034 0.146 2360 Planarity : 0.004 0.044 1617 Dihedral : 29.969 143.240 4274 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.61 % Allowed : 19.75 % 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: 2.17 (0.28), residues: 938 helix: 2.64 (0.21), residues: 596 sheet: -0.18 (0.69), residues: 61 loop : -0.91 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.009 0.001 TYR H 40 PHE 0.017 0.001 PHE L 506 TRP 0.009 0.002 TRP L 586 HIS 0.003 0.001 HIS L 430 Details of bonding type rmsd covalent geometry : bond 0.00306 (14496) covalent geometry : angle 0.56832 (20836) hydrogen bonds : bond 0.03167 ( 838) hydrogen bonds : angle 2.91648 ( 2129) Misc. bond : bond 0.00007 ( 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: 21 poor density : 172 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: C 73 ASN cc_start: 0.9127 (t0) cc_final: 0.8679 (t0) REVERT: E 64 LYS cc_start: 0.9066 (mttt) cc_final: 0.8846 (mtmm) REVERT: F 79 LYS cc_start: 0.9179 (mttm) cc_final: 0.8917 (mtpt) REVERT: G 73 ASN cc_start: 0.8803 (t0) cc_final: 0.8310 (t0) REVERT: H 33 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7305 (mtt180) REVERT: H 79 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8474 (mtm-85) REVERT: L 397 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6896 (tpp) REVERT: L 418 SER cc_start: 0.7564 (t) cc_final: 0.7192 (m) REVERT: L 449 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7350 (p90) REVERT: L 468 MET cc_start: 0.6659 (mpt) cc_final: 0.6101 (mmp) REVERT: L 534 MET cc_start: 0.6636 (ttt) cc_final: 0.6275 (tmm) REVERT: L 557 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (p0) REVERT: L 585 HIS cc_start: 0.8446 (m90) cc_final: 0.8084 (m90) outliers start: 21 outliers final: 7 residues processed: 180 average time/residue: 0.8552 time to fit residues: 164.0099 Evaluate side-chains 181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 449 HIS Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 557 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 ASN L 449 HIS ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066477 restraints weight = 28210.689| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.39 r_work: 0.2738 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14497 Z= 0.187 Angle : 0.586 12.474 20836 Z= 0.338 Chirality : 0.035 0.263 2360 Planarity : 0.004 0.045 1617 Dihedral : 29.998 142.628 4274 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 20.25 % Favored : 77.76 % 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: 2.07 (0.28), residues: 938 helix: 2.59 (0.21), residues: 596 sheet: -0.60 (0.65), residues: 67 loop : -0.92 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.009 0.001 TYR H 42 PHE 0.010 0.001 PHE L 506 TRP 0.010 0.002 TRP L 586 HIS 0.003 0.001 HIS L 430 Details of bonding type rmsd covalent geometry : bond 0.00419 (14496) covalent geometry : angle 0.58627 (20836) hydrogen bonds : bond 0.03436 ( 838) hydrogen bonds : angle 2.94986 ( 2129) Misc. bond : bond 0.00033 ( 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 183 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.437 Fit side-chains REVERT: C 20 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8680 (mtt-85) REVERT: C 64 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: C 73 ASN cc_start: 0.9134 (t0) cc_final: 0.8680 (t0) REVERT: E 64 LYS cc_start: 0.9094 (mttt) cc_final: 0.8878 (mtmm) REVERT: F 79 LYS cc_start: 0.9187 (mttm) cc_final: 0.8929 (mtpt) REVERT: G 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8334 (t0) REVERT: H 33 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7280 (mtt180) REVERT: L 397 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6870 (tpp) REVERT: L 418 SER cc_start: 0.7456 (t) cc_final: 0.7052 (m) REVERT: L 449 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7461 (p90) REVERT: L 468 MET cc_start: 0.6721 (mpt) cc_final: 0.6161 (mmp) REVERT: L 534 MET cc_start: 0.6720 (ttt) cc_final: 0.6359 (tmm) REVERT: L 557 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8647 (p0) REVERT: L 585 HIS cc_start: 0.8442 (m90) cc_final: 0.8058 (m90) outliers start: 16 outliers final: 7 residues processed: 175 average time/residue: 0.8817 time to fit residues: 164.0491 Evaluate side-chains 178 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 449 HIS Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 557 ASP 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: 0.9980 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067079 restraints weight = 28239.579| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.39 r_work: 0.2755 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14497 Z= 0.158 Angle : 0.585 12.707 20836 Z= 0.337 Chirality : 0.035 0.326 2360 Planarity : 0.004 0.045 1617 Dihedral : 29.993 142.794 4274 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 20.99 % Favored : 77.27 % 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: 2.08 (0.28), residues: 938 helix: 2.60 (0.21), residues: 596 sheet: -0.57 (0.66), residues: 67 loop : -0.93 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.010 0.001 TYR H 42 PHE 0.015 0.001 PHE L 506 TRP 0.009 0.002 TRP L 586 HIS 0.004 0.001 HIS L 430 Details of bonding type rmsd covalent geometry : bond 0.00346 (14496) covalent geometry : angle 0.58453 (20836) hydrogen bonds : bond 0.03307 ( 838) hydrogen bonds : angle 2.96672 ( 2129) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6184.70 seconds wall clock time: 105 minutes 32.92 seconds (6332.92 seconds total)