Starting phenix.real_space_refine on Wed Mar 4 21:38:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.map" model { file = "/net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea8_31040/03_2026/7ea8_31040.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4902 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 244 5.49 5 S 33 5.16 5 C 7305 2.51 5 N 2401 2.21 5 O 2879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12865 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 818 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2517 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 643 SG CYS L1529 40.601 58.945 52.919 1.00 46.92 S ATOM 672 SG CYS L1533 40.198 62.627 55.544 1.00 53.00 S ATOM 717 SG CYS L1539 40.330 62.668 51.612 1.00 47.82 S ATOM 416 SG CYS L1499 43.510 60.073 56.178 1.00 47.21 S ATOM 431 SG CYS L1501 46.699 61.864 55.722 1.00 51.47 S ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 569 SG CYS L1520 45.259 58.912 52.403 1.00 43.65 S ATOM 1863 SG CYS L1678 39.772 46.170 17.879 1.00 67.56 S ATOM 1909 SG CYS L1685 43.414 44.340 16.211 1.00 57.15 S Time building chain proxies: 2.51, per 1000 atoms: 0.20 Number of scatterers: 12865 At special positions: 0 Unit cell: (132, 88, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 244 15.00 O 2879 8.00 N 2401 7.00 C 7305 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: 0.72 Conformation dependent library (CDL) restraints added in 401.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1801 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1539 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1533 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1529 " pdb=" ZN L1802 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1520 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1499 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1501 " pdb=" ZN L1803 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1678 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1685 " Number of angles added : 12 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 57.7% alpha, 4.6% beta 121 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'L' and resid 1520 through 1525 removed outlier: 3.660A pdb=" N LEU L1524 " --> pdb=" O CYS L1520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU L1525 " --> pdb=" O LEU L1521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1520 through 1525' Processing helix chain 'L' and resid 1535 through 1539 removed outlier: 4.046A pdb=" N CYS L1539 " --> pdb=" O GLY L1536 " (cutoff:3.500A) Processing helix chain 'L' and resid 1585 through 1597 removed outlier: 4.080A pdb=" N PHE L1589 " --> pdb=" O ASP L1585 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS L1590 " --> pdb=" O HIS L1586 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L1591 " --> pdb=" O LYS L1587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L1594 " --> pdb=" O LYS L1590 " (cutoff:3.500A) Processing helix chain 'L' and resid 1598 through 1600 No H-bonds generated for 'chain 'L' and resid 1598 through 1600' Processing helix chain 'L' and resid 1622 through 1626 removed outlier: 3.531A pdb=" N ARG L1625 " --> pdb=" O ASN L1622 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE L1626 " --> pdb=" O CYS L1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1622 through 1626' Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.597A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.657A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.849A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.748A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.996A 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 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.706A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.815A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.659A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.905A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.850A 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 75 removed outlier: 3.792A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.044A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.718A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (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 76 removed outlier: 4.026A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.978A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.912A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.718A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 1556 through 1558 removed outlier: 4.337A pdb=" N GLU L1558 " --> pdb=" O GLY L1561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 1575 through 1578 removed outlier: 6.954A pdb=" N PHE L1650 " --> pdb=" O VAL L1576 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU L1578 " --> pdb=" O VAL L1648 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL L1648 " --> pdb=" O GLU L1578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 1582 through 1583 Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.322A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.110A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.904A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.302A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 392 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2951 1.34 - 1.46: 4033 1.46 - 1.58: 6070 1.58 - 1.70: 486 1.70 - 1.82: 49 Bond restraints: 13589 Sorted by residual: bond pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C8 SAM L1804 " pdb=" N7 SAM L1804 " ideal model delta sigma weight residual 1.298 1.353 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C2 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C6 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.337 1.380 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 ... (remaining 13584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18677 1.70 - 3.39: 633 3.39 - 5.09: 46 5.09 - 6.79: 14 6.79 - 8.48: 5 Bond angle restraints: 19375 Sorted by residual: angle pdb=" N SER L1490 " pdb=" CA SER L1490 " pdb=" C SER L1490 " ideal model delta sigma weight residual 110.97 114.53 -3.56 1.09e+00 8.42e-01 1.07e+01 angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 113.39 108.67 4.72 1.47e+00 4.63e-01 1.03e+01 angle pdb=" C LYS L1489 " pdb=" N SER L1490 " pdb=" CA SER L1490 " ideal model delta sigma weight residual 120.65 124.65 -4.00 1.32e+00 5.74e-01 9.18e+00 angle pdb=" N1 SAM L1804 " pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 128.51 120.03 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" O SAM L1804 " pdb=" C SAM L1804 " pdb=" OXT SAM L1804 " ideal model delta sigma weight residual 126.77 118.53 8.24 3.00e+00 1.11e-01 7.54e+00 ... (remaining 19370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 6140 27.88 - 55.77: 1308 55.77 - 83.65: 111 83.65 - 111.53: 0 111.53 - 139.41: 3 Dihedral angle restraints: 7562 sinusoidal: 4718 harmonic: 2844 Sorted by residual: dihedral pdb=" CA TYR L1666 " pdb=" C TYR L1666 " pdb=" N GLN L1667 " pdb=" CA GLN L1667 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU L1478 " pdb=" C GLU L1478 " pdb=" N ASN L1479 " pdb=" CA ASN L1479 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 80.59 139.41 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 7559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1775 0.052 - 0.104: 326 0.104 - 0.156: 67 0.156 - 0.208: 4 0.208 - 0.260: 1 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE L1494 " pdb=" CA ILE L1494 " pdb=" CG1 ILE L1494 " pdb=" CG2 ILE L1494 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 2170 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 103 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO D 103 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3109 2.82 - 3.34: 10018 3.34 - 3.86: 22773 3.86 - 4.38: 26823 4.38 - 4.90: 39763 Nonbonded interactions: 102486 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.306 3.040 nonbonded pdb=" ND2 ASN L1634 " pdb=" O GLU L1661 " model vdw 2.379 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.381 3.120 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.382 3.040 nonbonded pdb=" O GLU L1578 " pdb=" ND2 ASN L1622 " model vdw 2.387 3.120 ... (remaining 102481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 76 or resid 78 through 133)) selection = chain 'E' } 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 35 through 123) 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.010 0.487 13600 Z= 0.382 Angle : 0.791 27.780 19387 Z= 0.426 Chirality : 0.043 0.260 2173 Planarity : 0.006 0.051 1621 Dihedral : 24.060 139.413 5732 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -3.23 (0.21), residues: 964 helix: -1.58 (0.17), residues: 540 sheet: -2.04 (0.90), residues: 31 loop : -2.88 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.024 0.002 TYR H 42 PHE 0.021 0.002 PHE L1664 TRP 0.014 0.002 TRP L1640 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00382 (13589) covalent geometry : angle 0.70929 (19375) hydrogen bonds : bond 0.10867 ( 706) hydrogen bonds : angle 4.47227 ( 1783) metal coordination : bond 0.35222 ( 10) metal coordination : angle 14.08458 ( 12) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: L 1486 LYS cc_start: 0.4525 (pmtt) cc_final: 0.4285 (mmtt) REVERT: L 1599 ASN cc_start: 0.4018 (m-40) cc_final: 0.3669 (t0) REVERT: B 68 ASP cc_start: 0.7662 (m-30) cc_final: 0.7439 (m-30) REVERT: C 75 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8335 (mmtt) REVERT: D 62 MET cc_start: 0.8493 (mmm) cc_final: 0.8249 (mmm) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2031 time to fit residues: 59.6973 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1545 GLN L1548 GLN ** L1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1667 GLN L1684 ASN A 39 HIS A 68 GLN B 93 GLN C 68 ASN E 68 GLN F 27 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.185802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144491 restraints weight = 14056.375| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.21 r_work: 0.3112 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13600 Z= 0.258 Angle : 0.668 8.973 19387 Z= 0.378 Chirality : 0.041 0.166 2173 Planarity : 0.006 0.049 1621 Dihedral : 28.851 147.552 3773 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.21 % Allowed : 8.44 % Favored : 90.35 % 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: -1.32 (0.25), residues: 964 helix: 0.39 (0.22), residues: 555 sheet: -1.76 (0.88), residues: 33 loop : -2.80 (0.26), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.017 0.002 TYR C 50 PHE 0.032 0.003 PHE C 25 TRP 0.012 0.003 TRP L1562 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00597 (13589) covalent geometry : angle 0.65500 (19375) hydrogen bonds : bond 0.08119 ( 706) hydrogen bonds : angle 3.17712 ( 1783) metal coordination : bond 0.01418 ( 10) metal coordination : angle 5.28113 ( 12) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.266 Fit side-chains REVERT: L 1514 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5741 (pp) REVERT: A 73 GLU cc_start: 0.8313 (tt0) cc_final: 0.8104 (tt0) REVERT: A 106 ASP cc_start: 0.7836 (m-30) cc_final: 0.7625 (m-30) REVERT: A 115 LYS cc_start: 0.7977 (mttp) cc_final: 0.7604 (mtmm) REVERT: C 75 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8765 (mmtt) REVERT: H 47 GLN cc_start: 0.8218 (mt0) cc_final: 0.7859 (mt0) REVERT: H 63 ASN cc_start: 0.8589 (t160) cc_final: 0.8357 (m-40) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.1747 time to fit residues: 35.9159 Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1514 ILE Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 26 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1599 ASN ** H 63 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.188607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143481 restraints weight = 14265.003| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.19 r_work: 0.3152 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13600 Z= 0.173 Angle : 0.562 6.384 19387 Z= 0.329 Chirality : 0.036 0.142 2173 Planarity : 0.004 0.048 1621 Dihedral : 28.679 146.810 3773 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.57 % Allowed : 9.65 % Favored : 88.78 % 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: -0.27 (0.27), residues: 964 helix: 1.49 (0.23), residues: 541 sheet: -1.58 (0.97), residues: 28 loop : -2.61 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.010 0.001 TYR L1596 PHE 0.025 0.002 PHE L1589 TRP 0.007 0.001 TRP L1562 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00383 (13589) covalent geometry : angle 0.55578 (19375) hydrogen bonds : bond 0.05987 ( 706) hydrogen bonds : angle 2.86619 ( 1783) metal coordination : bond 0.00545 ( 10) metal coordination : angle 3.47734 ( 12) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.356 Fit side-chains REVERT: A 105 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: A 115 LYS cc_start: 0.7663 (mttp) cc_final: 0.7401 (mtmm) REVERT: B 92 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7667 (ttp80) REVERT: D 42 TYR cc_start: 0.8370 (t80) cc_final: 0.8151 (t80) outliers start: 13 outliers final: 8 residues processed: 150 average time/residue: 0.1679 time to fit residues: 32.6706 Evaluate side-chains 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.190336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146778 restraints weight = 14237.614| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.15 r_work: 0.3212 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13600 Z= 0.142 Angle : 0.537 7.898 19387 Z= 0.318 Chirality : 0.035 0.137 2173 Planarity : 0.004 0.042 1621 Dihedral : 28.633 147.424 3773 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.97 % Allowed : 11.22 % Favored : 87.82 % 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: 0.28 (0.28), residues: 964 helix: 1.99 (0.23), residues: 540 sheet: -1.30 (1.00), residues: 28 loop : -2.45 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.008 0.001 TYR L1596 PHE 0.014 0.001 PHE L1589 TRP 0.009 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00295 (13589) covalent geometry : angle 0.53260 (19375) hydrogen bonds : bond 0.05178 ( 706) hydrogen bonds : angle 2.74118 ( 1783) metal coordination : bond 0.00445 ( 10) metal coordination : angle 2.82778 ( 12) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.389 Fit side-chains REVERT: A 105 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: A 115 LYS cc_start: 0.7487 (mttp) cc_final: 0.7234 (mtmm) REVERT: A 129 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7807 (ttt180) REVERT: B 92 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7785 (ttp80) REVERT: D 42 TYR cc_start: 0.8276 (t80) cc_final: 0.8061 (t80) REVERT: G 108 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7778 (mp) outliers start: 8 outliers final: 4 residues processed: 140 average time/residue: 0.1719 time to fit residues: 31.1626 Evaluate side-chains 142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1541 ASN L1548 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.189871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145487 restraints weight = 14348.499| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.14 r_work: 0.3167 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13600 Z= 0.153 Angle : 0.527 5.895 19387 Z= 0.313 Chirality : 0.035 0.136 2173 Planarity : 0.004 0.042 1621 Dihedral : 28.550 147.499 3773 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.21 % Allowed : 11.82 % Favored : 86.97 % 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: 0.66 (0.28), residues: 964 helix: 2.27 (0.23), residues: 539 sheet: -1.09 (1.02), residues: 28 loop : -2.24 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.008 0.001 TYR L1596 PHE 0.014 0.002 PHE L1589 TRP 0.006 0.001 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00332 (13589) covalent geometry : angle 0.52416 (19375) hydrogen bonds : bond 0.05268 ( 706) hydrogen bonds : angle 2.68559 ( 1783) metal coordination : bond 0.00327 ( 10) metal coordination : angle 2.27522 ( 12) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.384 Fit side-chains REVERT: L 1504 LEU cc_start: 0.3265 (tt) cc_final: 0.2546 (tp) REVERT: L 1582 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5600 (tp30) REVERT: A 105 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: A 115 LYS cc_start: 0.7562 (mttp) cc_final: 0.7269 (mtmm) REVERT: A 129 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7901 (ttt180) REVERT: B 92 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: C 36 LYS cc_start: 0.8502 (mptt) cc_final: 0.8285 (mptt) REVERT: D 42 TYR cc_start: 0.8338 (t80) cc_final: 0.8006 (t80) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.1597 time to fit residues: 30.2875 Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144953 restraints weight = 14120.622| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.33 r_work: 0.3109 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13600 Z= 0.161 Angle : 0.527 6.019 19387 Z= 0.313 Chirality : 0.035 0.135 2173 Planarity : 0.004 0.042 1621 Dihedral : 28.509 147.629 3773 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.45 % Allowed : 11.82 % Favored : 86.73 % 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: 0.69 (0.28), residues: 964 helix: 2.26 (0.23), residues: 546 sheet: -1.08 (1.01), residues: 28 loop : -2.23 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.007 0.001 TYR L1596 PHE 0.015 0.001 PHE L1589 TRP 0.010 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00352 (13589) covalent geometry : angle 0.52404 (19375) hydrogen bonds : bond 0.05457 ( 706) hydrogen bonds : angle 2.69541 ( 1783) metal coordination : bond 0.00399 ( 10) metal coordination : angle 2.37379 ( 12) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.311 Fit side-chains REVERT: L 1497 MET cc_start: 0.5631 (mmp) cc_final: 0.4834 (mpp) REVERT: L 1582 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5629 (tp30) REVERT: L 1638 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: A 105 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: A 115 LYS cc_start: 0.7675 (mttp) cc_final: 0.7348 (mtmm) REVERT: A 129 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8022 (ttt180) REVERT: B 92 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: C 36 LYS cc_start: 0.8508 (mptt) cc_final: 0.8289 (mptt) REVERT: C 40 SER cc_start: 0.8868 (p) cc_final: 0.8668 (p) REVERT: D 42 TYR cc_start: 0.8370 (t80) cc_final: 0.8013 (t80) REVERT: H 76 GLU cc_start: 0.8161 (tp30) cc_final: 0.7952 (tp30) outliers start: 12 outliers final: 9 residues processed: 144 average time/residue: 0.1625 time to fit residues: 30.5572 Evaluate side-chains 147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.187995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142795 restraints weight = 14119.732| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.11 r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13600 Z= 0.180 Angle : 0.548 6.589 19387 Z= 0.323 Chirality : 0.036 0.145 2173 Planarity : 0.004 0.043 1621 Dihedral : 28.520 147.353 3773 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.57 % Allowed : 12.42 % Favored : 86.01 % 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: 0.63 (0.28), residues: 964 helix: 2.18 (0.23), residues: 546 sheet: -1.04 (1.02), residues: 28 loop : -2.22 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.010 0.001 TYR H 42 PHE 0.015 0.002 PHE L1589 TRP 0.010 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00403 (13589) covalent geometry : angle 0.54481 (19375) hydrogen bonds : bond 0.06053 ( 706) hydrogen bonds : angle 2.76932 ( 1783) metal coordination : bond 0.00437 ( 10) metal coordination : angle 2.57721 ( 12) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.259 Fit side-chains REVERT: L 1478 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6090 (tm-30) REVERT: L 1497 MET cc_start: 0.5846 (mmp) cc_final: 0.5047 (mpp) REVERT: L 1504 LEU cc_start: 0.3290 (tt) cc_final: 0.2530 (tp) REVERT: L 1582 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5714 (tp30) REVERT: L 1638 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: A 105 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: A 115 LYS cc_start: 0.7725 (mttp) cc_final: 0.7416 (mtmm) REVERT: A 129 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7844 (ttt180) REVERT: B 92 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7906 (ttp80) REVERT: C 36 LYS cc_start: 0.8490 (mptt) cc_final: 0.8274 (mptt) REVERT: D 42 TYR cc_start: 0.8300 (t80) cc_final: 0.7948 (t80) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.1647 time to fit residues: 31.5351 Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.187417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141127 restraints weight = 13989.284| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.10 r_work: 0.3153 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13600 Z= 0.182 Angle : 0.550 6.432 19387 Z= 0.324 Chirality : 0.036 0.143 2173 Planarity : 0.004 0.043 1621 Dihedral : 28.513 147.404 3773 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.45 % Allowed : 13.03 % Favored : 85.52 % 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: 0.60 (0.28), residues: 964 helix: 2.14 (0.23), residues: 546 sheet: -0.99 (1.03), residues: 28 loop : -2.20 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.010 0.001 TYR H 42 PHE 0.016 0.002 PHE L1589 TRP 0.008 0.002 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00409 (13589) covalent geometry : angle 0.54671 (19375) hydrogen bonds : bond 0.06101 ( 706) hydrogen bonds : angle 2.78897 ( 1783) metal coordination : bond 0.00437 ( 10) metal coordination : angle 2.60631 ( 12) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.375 Fit side-chains REVERT: L 1497 MET cc_start: 0.5905 (mmp) cc_final: 0.4885 (mpp) REVERT: L 1504 LEU cc_start: 0.3244 (tt) cc_final: 0.2491 (tp) REVERT: L 1582 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5752 (tp30) REVERT: L 1638 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: A 105 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: A 115 LYS cc_start: 0.7743 (mttp) cc_final: 0.7433 (mtmm) REVERT: B 92 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: C 36 LYS cc_start: 0.8496 (mptt) cc_final: 0.8281 (mptt) REVERT: D 42 TYR cc_start: 0.8319 (t80) cc_final: 0.7967 (t80) outliers start: 12 outliers final: 9 residues processed: 146 average time/residue: 0.1544 time to fit residues: 29.4612 Evaluate side-chains 147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1622 ASN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143888 restraints weight = 14161.404| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.14 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13600 Z= 0.167 Angle : 0.540 6.325 19387 Z= 0.320 Chirality : 0.035 0.138 2173 Planarity : 0.004 0.043 1621 Dihedral : 28.471 147.593 3773 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.69 % Allowed : 12.91 % Favored : 85.40 % 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: 0.75 (0.28), residues: 964 helix: 2.26 (0.23), residues: 546 sheet: -0.92 (1.03), residues: 28 loop : -2.12 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 35 TYR 0.011 0.001 TYR H 42 PHE 0.016 0.002 PHE L1589 TRP 0.008 0.001 TRP L1562 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00367 (13589) covalent geometry : angle 0.53593 (19375) hydrogen bonds : bond 0.05664 ( 706) hydrogen bonds : angle 2.72678 ( 1783) metal coordination : bond 0.00411 ( 10) metal coordination : angle 2.60397 ( 12) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.276 Fit side-chains REVERT: L 1497 MET cc_start: 0.5737 (mmp) cc_final: 0.4686 (mpp) REVERT: L 1504 LEU cc_start: 0.3529 (tt) cc_final: 0.2812 (tp) REVERT: L 1582 GLU cc_start: 0.6341 (mt-10) cc_final: 0.5746 (tp30) REVERT: L 1638 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: A 105 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: A 115 LYS cc_start: 0.7712 (mttp) cc_final: 0.7392 (mtmm) REVERT: A 129 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7837 (ttt180) REVERT: B 27 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8237 (mm-40) REVERT: B 92 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7922 (ttp80) REVERT: C 36 LYS cc_start: 0.8488 (mptt) cc_final: 0.8280 (mptt) REVERT: C 116 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7793 (pp) REVERT: D 42 TYR cc_start: 0.8277 (t80) cc_final: 0.7920 (t80) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.1638 time to fit residues: 31.9052 Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145289 restraints weight = 14078.143| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.27 r_work: 0.3148 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13600 Z= 0.158 Angle : 0.534 6.229 19387 Z= 0.317 Chirality : 0.035 0.145 2173 Planarity : 0.004 0.042 1621 Dihedral : 28.462 147.711 3773 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.69 % Allowed : 13.03 % Favored : 85.28 % 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: 0.82 (0.28), residues: 964 helix: 2.30 (0.23), residues: 546 sheet: -0.85 (1.00), residues: 28 loop : -2.08 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 35 TYR 0.013 0.001 TYR H 42 PHE 0.015 0.001 PHE L1589 TRP 0.009 0.001 TRP L1562 HIS 0.008 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00343 (13589) covalent geometry : angle 0.53056 (19375) hydrogen bonds : bond 0.05508 ( 706) hydrogen bonds : angle 2.71047 ( 1783) metal coordination : bond 0.00407 ( 10) metal coordination : angle 2.55003 ( 12) Misc. bond : bond 0.00013 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.391 Fit side-chains REVERT: L 1497 MET cc_start: 0.5870 (mmp) cc_final: 0.4804 (mpp) REVERT: L 1504 LEU cc_start: 0.3498 (tt) cc_final: 0.2783 (tp) REVERT: L 1582 GLU cc_start: 0.6357 (mt-10) cc_final: 0.5761 (tp30) REVERT: L 1638 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: A 105 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: A 115 LYS cc_start: 0.7679 (mttp) cc_final: 0.7358 (mtmm) REVERT: A 129 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7944 (ttt180) REVERT: B 27 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8273 (mm-40) REVERT: B 92 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: C 36 LYS cc_start: 0.8502 (mptt) cc_final: 0.8295 (mptt) REVERT: C 116 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (pp) REVERT: D 42 TYR cc_start: 0.8310 (t80) cc_final: 0.7942 (t80) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.1653 time to fit residues: 31.6046 Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain L residue 1642 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142758 restraints weight = 14175.192| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.13 r_work: 0.3162 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13600 Z= 0.179 Angle : 0.550 6.191 19387 Z= 0.325 Chirality : 0.036 0.127 2173 Planarity : 0.004 0.043 1621 Dihedral : 28.476 147.452 3773 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.57 % Allowed : 13.51 % Favored : 84.92 % 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: 0.70 (0.28), residues: 964 helix: 2.20 (0.23), residues: 546 sheet: -0.60 (1.16), residues: 18 loop : -2.13 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.008 0.001 TYR D 121 PHE 0.015 0.002 PHE L1589 TRP 0.008 0.001 TRP L1562 HIS 0.007 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00399 (13589) covalent geometry : angle 0.54625 (19375) hydrogen bonds : bond 0.06039 ( 706) hydrogen bonds : angle 2.77833 ( 1783) metal coordination : bond 0.00412 ( 10) metal coordination : angle 2.53909 ( 12) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.03 seconds wall clock time: 46 minutes 16.09 seconds (2776.09 seconds total)