Starting phenix.real_space_refine on Sun Nov 17 05:48:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/11_2024/8ox1_17252.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 293 5.49 5 S 18 5.16 5 C 7423 2.51 5 N 2502 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13258 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 511 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "M" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 575 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.71, per 1000 atoms: 0.66 Number of scatterers: 13258 At special positions: 0 Unit cell: (101.598, 117.292, 128.03, 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 18 16.00 P 293 15.00 O 3022 8.00 N 2502 7.00 C 7423 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=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 69.5% alpha, 2.7% beta 140 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 6.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.552A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.614A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.524A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.208A 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 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.367A 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'L' and resid 385 through 398 removed outlier: 3.761A pdb=" N LEU L 391 " --> pdb=" O GLU L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 410 Processing helix chain 'L' and resid 416 through 431 Processing helix chain 'M' and resid 384 through 398 Processing helix chain 'M' and resid 402 through 410 Processing helix chain 'M' and resid 416 through 430 Processing sheet with id=AA1, 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=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: 6.738A 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: 7.099A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.685A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.919A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.279A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 462 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 3.71 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: 1672 1.32 - 1.45: 5160 1.45 - 1.57: 6628 1.57 - 1.69: 582 1.69 - 1.82: 32 Bond restraints: 14074 Sorted by residual: bond pdb=" CA LYS L 411 " pdb=" CB LYS L 411 " ideal model delta sigma weight residual 1.525 1.438 0.087 1.29e-02 6.01e+03 4.58e+01 bond pdb=" O2P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.498 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.11e+01 bond pdb=" CA GLU L 386 " pdb=" CB GLU L 386 " ideal model delta sigma weight residual 1.530 1.444 0.086 1.56e-02 4.11e+03 3.04e+01 bond pdb=" O3P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 14069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 19160 2.22 - 4.45: 998 4.45 - 6.67: 51 6.67 - 8.89: 4 8.89 - 11.12: 2 Bond angle restraints: 20215 Sorted by residual: angle pdb=" C GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 110.79 117.70 -6.91 1.66e+00 3.63e-01 1.73e+01 angle pdb=" O3' DC I -58 " pdb=" C3' DC I -58 " pdb=" C2' DC I -58 " ideal model delta sigma weight residual 111.50 117.72 -6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" N LEU M 391 " pdb=" CA LEU M 391 " pdb=" C LEU M 391 " ideal model delta sigma weight residual 111.07 106.75 4.32 1.07e+00 8.73e-01 1.63e+01 angle pdb=" N GLU L 386 " pdb=" CA GLU L 386 " pdb=" C GLU L 386 " ideal model delta sigma weight residual 111.11 115.85 -4.74 1.20e+00 6.94e-01 1.56e+01 angle pdb=" N SER H 120 " pdb=" CA SER H 120 " pdb=" C SER H 120 " ideal model delta sigma weight residual 111.07 115.11 -4.04 1.07e+00 8.73e-01 1.43e+01 ... (remaining 20210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.35: 6328 33.35 - 66.69: 1450 66.69 - 100.04: 11 100.04 - 133.39: 0 133.39 - 166.74: 2 Dihedral angle restraints: 7791 sinusoidal: 5168 harmonic: 2623 Sorted by residual: dihedral pdb=" C GLU M 386 " pdb=" N GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta harmonic sigma weight residual -122.60 -133.69 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C4' DT I 35 " pdb=" C3' DT I 35 " pdb=" O3' DT I 35 " pdb=" P DA I 36 " ideal model delta sinusoidal sigma weight residual 220.00 53.26 166.74 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" O3' DA I 49 " pdb=" P DC I 50 " ideal model delta sinusoidal sigma weight residual 220.00 81.40 138.60 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2087 0.102 - 0.204: 169 0.204 - 0.306: 8 0.306 - 0.409: 2 0.409 - 0.511: 1 Chirality restraints: 2267 Sorted by residual: chirality pdb=" CA GLU M 386 " pdb=" N GLU M 386 " pdb=" C GLU M 386 " pdb=" CB GLU M 386 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" CA GLU L 386 " pdb=" N GLU L 386 " pdb=" C GLU L 386 " pdb=" CB GLU L 386 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA LYS L 429 " pdb=" N LYS L 429 " pdb=" C LYS L 429 " pdb=" CB LYS L 429 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2264 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -21 " 0.046 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG J -21 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -21 " -0.018 2.00e-02 2.50e+03 pdb=" N7 DG J -21 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DG J -21 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG J -21 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG J -21 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG J -21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J -21 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG J -21 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DG J -21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J -21 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " -0.043 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" N1 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " -0.027 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -35 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.30e+00 pdb=" N9 DA J -35 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DA J -35 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J -35 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA J -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA J -35 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA J -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA J -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA J -35 " -0.012 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3474 2.84 - 3.36: 11613 3.36 - 3.87: 26368 3.87 - 4.39: 30725 4.39 - 4.90: 42295 Nonbonded interactions: 114475 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DG J 70 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU M 387 " pdb=" N ASN M 413 " model vdw 2.336 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.349 3.040 nonbonded pdb=" O ARG L 380 " pdb=" NE2 GLN L 381 " model vdw 2.403 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.418 3.040 ... (remaining 114470 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' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 25 through 122) } ncs_group { reference = (chain 'L' and resid 377 through 433) selection = (chain 'M' and resid 377 through 433) } 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=0.00 max=1.00 mean=0.99 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: 3.380 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.780 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.009 0.112 14074 Z= 0.511 Angle : 1.054 11.117 20215 Z= 0.678 Chirality : 0.063 0.511 2267 Planarity : 0.006 0.045 1542 Dihedral : 25.999 166.737 6097 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 879 helix: 1.24 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP M 385 HIS 0.008 0.002 HIS D 46 PHE 0.020 0.005 PHE A 104 TYR 0.028 0.005 TYR G 50 ARG 0.039 0.002 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8853 (mtt) cc_final: 0.8648 (mtp) REVERT: B 95 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7915 (mtp85) REVERT: C 36 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8905 (mmtt) REVERT: D 30 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6942 (mtp180) REVERT: D 39 TYR cc_start: 0.8633 (t80) cc_final: 0.8384 (t80) REVERT: D 96 ARG cc_start: 0.8831 (mtt-85) cc_final: 0.8505 (mtt-85) REVERT: E 56 LYS cc_start: 0.9195 (tttm) cc_final: 0.8801 (ttmt) REVERT: E 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8224 (pm20) REVERT: E 64 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8439 (mtmt) REVERT: G 11 ARG cc_start: 0.6623 (mtp-110) cc_final: 0.6320 (mtp180) REVERT: H 119 THR cc_start: 0.9121 (m) cc_final: 0.8911 (m) REVERT: L 380 ARG cc_start: 0.4563 (mmt90) cc_final: 0.4314 (ttm170) REVERT: L 406 ILE cc_start: 0.5969 (mt) cc_final: 0.5767 (tp) REVERT: L 423 ARG cc_start: 0.7788 (tpt170) cc_final: 0.7331 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 1.9674 time to fit residues: 372.2572 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14074 Z= 0.203 Angle : 0.561 8.874 20215 Z= 0.336 Chirality : 0.033 0.133 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.915 165.583 4236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.57 % Allowed : 8.66 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 879 helix: 2.38 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -0.52 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.018 0.001 PHE A 104 TYR 0.013 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8767 (tttm) cc_final: 0.8483 (ttpp) REVERT: D 26 ARG cc_start: 0.6506 (ttp-170) cc_final: 0.6299 (ttt180) REVERT: D 30 ARG cc_start: 0.7562 (mmt90) cc_final: 0.6988 (mtp180) REVERT: D 31 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7925 (mmmm) REVERT: D 96 ARG cc_start: 0.8766 (mtt-85) cc_final: 0.8464 (mtt-85) REVERT: E 56 LYS cc_start: 0.9093 (tttm) cc_final: 0.8766 (ttmt) REVERT: E 64 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8464 (mtmt) REVERT: F 22 LEU cc_start: 0.6929 (mt) cc_final: 0.6597 (mp) REVERT: G 15 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8304 (tttp) REVERT: L 423 ARG cc_start: 0.7830 (tpt170) cc_final: 0.7384 (tpm170) REVERT: L 427 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6603 (mpt) REVERT: M 431 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8584 (mtmm) REVERT: M 432 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8494 (mp) outliers start: 12 outliers final: 2 residues processed: 159 average time/residue: 1.7744 time to fit residues: 300.4009 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 432 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 68 GLN M 402 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14074 Z= 0.147 Angle : 0.509 7.017 20215 Z= 0.308 Chirality : 0.031 0.137 2267 Planarity : 0.003 0.039 1542 Dihedral : 29.587 165.088 4236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.18 % Allowed : 10.37 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.27), residues: 879 helix: 2.84 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 383 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE A 104 TYR 0.013 0.001 TYR D 37 ARG 0.006 0.000 ARG M 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8846 (tttm) cc_final: 0.8560 (ttpp) REVERT: A 120 MET cc_start: 0.8671 (mtt) cc_final: 0.8446 (mtp) REVERT: A 129 ARG cc_start: 0.8723 (tpt90) cc_final: 0.8407 (tpt-90) REVERT: B 25 ASN cc_start: 0.8722 (m110) cc_final: 0.8454 (m-40) REVERT: D 30 ARG cc_start: 0.7529 (mmt90) cc_final: 0.6943 (mtp180) REVERT: D 31 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7936 (mmmm) REVERT: D 96 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8511 (tpp80) REVERT: E 59 GLU cc_start: 0.8440 (pm20) cc_final: 0.8020 (pm20) REVERT: E 64 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8465 (mtmt) REVERT: F 22 LEU cc_start: 0.6792 (mt) cc_final: 0.6453 (mp) REVERT: G 15 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8204 (tttp) REVERT: L 423 ARG cc_start: 0.7947 (tpt170) cc_final: 0.7415 (tpm170) REVERT: M 432 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8551 (mp) outliers start: 9 outliers final: 2 residues processed: 159 average time/residue: 1.8508 time to fit residues: 312.9075 Evaluate side-chains 137 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 432 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 68 GLN H 44 GLN H 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14074 Z= 0.334 Angle : 0.580 8.216 20215 Z= 0.342 Chirality : 0.036 0.148 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.163 172.428 4236 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 12.07 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.27), residues: 879 helix: 2.60 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.06 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 403 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.002 PHE E 78 TYR 0.012 0.002 TYR D 37 ARG 0.005 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.082 Fit side-chains REVERT: A 129 ARG cc_start: 0.8804 (tpt90) cc_final: 0.8451 (tpt-90) REVERT: C 73 ASN cc_start: 0.8106 (t160) cc_final: 0.7858 (t160) REVERT: D 30 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7013 (mtp180) REVERT: D 31 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7958 (mmmm) REVERT: D 96 ARG cc_start: 0.8774 (mtt-85) cc_final: 0.8467 (mtt-85) REVERT: E 38 PRO cc_start: 0.8387 (Cg_exo) cc_final: 0.8154 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8636 (pm20) cc_final: 0.8278 (pm20) REVERT: E 64 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8488 (mtmt) REVERT: E 120 MET cc_start: 0.8419 (mmt) cc_final: 0.8167 (mtp) REVERT: F 22 LEU cc_start: 0.6931 (mt) cc_final: 0.6630 (mp) REVERT: H 65 ASP cc_start: 0.9171 (t0) cc_final: 0.8906 (t0) REVERT: L 423 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7589 (tpm170) REVERT: M 432 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (mp) outliers start: 16 outliers final: 5 residues processed: 144 average time/residue: 1.7932 time to fit residues: 275.2189 Evaluate side-chains 140 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14074 Z= 0.266 Angle : 0.564 8.834 20215 Z= 0.333 Chirality : 0.035 0.146 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.133 172.405 4236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.49 % Allowed : 12.07 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.27), residues: 879 helix: 2.59 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.004 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.990 Fit side-chains REVERT: A 129 ARG cc_start: 0.8800 (tpt90) cc_final: 0.8398 (tpt-90) REVERT: C 73 ASN cc_start: 0.8095 (t0) cc_final: 0.7812 (t160) REVERT: D 30 ARG cc_start: 0.7546 (mmt90) cc_final: 0.7024 (mtp180) REVERT: D 31 LYS cc_start: 0.8368 (mtpp) cc_final: 0.7950 (mmmm) REVERT: E 38 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.8149 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8647 (pm20) cc_final: 0.8274 (pm20) REVERT: E 64 LYS cc_start: 0.8896 (mmtp) cc_final: 0.8478 (mtmt) REVERT: F 22 LEU cc_start: 0.6914 (mt) cc_final: 0.6586 (mp) REVERT: G 15 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8147 (tttp) REVERT: H 65 ASP cc_start: 0.9164 (t0) cc_final: 0.8900 (t0) REVERT: L 423 ARG cc_start: 0.7803 (tpt170) cc_final: 0.7595 (tpm170) REVERT: M 432 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8546 (mp) outliers start: 19 outliers final: 8 residues processed: 148 average time/residue: 1.7977 time to fit residues: 283.3492 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 426 THR Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14074 Z= 0.175 Angle : 0.549 10.638 20215 Z= 0.325 Chirality : 0.033 0.146 2267 Planarity : 0.004 0.040 1542 Dihedral : 30.091 172.223 4236 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.84 % Allowed : 13.12 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.27), residues: 879 helix: 2.71 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.08 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.096 Fit side-chains REVERT: A 129 ARG cc_start: 0.8785 (tpt90) cc_final: 0.8393 (tpt-90) REVERT: C 73 ASN cc_start: 0.8080 (t0) cc_final: 0.7781 (t160) REVERT: D 30 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7026 (mtp180) REVERT: D 31 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7932 (mmmm) REVERT: E 38 PRO cc_start: 0.8401 (Cg_exo) cc_final: 0.8171 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8634 (pm20) cc_final: 0.8268 (pm20) REVERT: E 64 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8466 (mtmt) REVERT: E 120 MET cc_start: 0.8299 (mmt) cc_final: 0.7999 (mtp) REVERT: F 22 LEU cc_start: 0.6894 (mt) cc_final: 0.6570 (mp) REVERT: G 15 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8088 (tttp) REVERT: H 65 ASP cc_start: 0.9148 (t0) cc_final: 0.8899 (t0) REVERT: L 432 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6852 (tt) REVERT: M 432 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 14 outliers final: 6 residues processed: 145 average time/residue: 1.7935 time to fit residues: 277.2887 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 432 LEU Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14074 Z= 0.186 Angle : 0.537 9.999 20215 Z= 0.319 Chirality : 0.032 0.143 2267 Planarity : 0.004 0.073 1542 Dihedral : 29.952 172.053 4236 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.27), residues: 879 helix: 2.76 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.12 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 383 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.011 0.001 TYR D 37 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.890 Fit side-chains REVERT: A 129 ARG cc_start: 0.8779 (tpt90) cc_final: 0.8390 (tpt-90) REVERT: C 73 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7792 (t160) REVERT: D 30 ARG cc_start: 0.7546 (mmt90) cc_final: 0.7029 (mtp180) REVERT: D 31 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7872 (mmmm) REVERT: E 38 PRO cc_start: 0.8328 (Cg_exo) cc_final: 0.8093 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8607 (pm20) cc_final: 0.8239 (pm20) REVERT: E 64 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8470 (mtmt) REVERT: F 22 LEU cc_start: 0.6878 (mt) cc_final: 0.6563 (mp) REVERT: G 15 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8065 (tttp) REVERT: L 423 ARG cc_start: 0.7732 (tpm170) cc_final: 0.7128 (tpm170) REVERT: L 427 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6548 (mpt) outliers start: 16 outliers final: 6 residues processed: 145 average time/residue: 1.7959 time to fit residues: 277.0386 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14074 Z= 0.309 Angle : 0.578 9.907 20215 Z= 0.339 Chirality : 0.036 0.148 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.075 174.435 4236 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.84 % Allowed : 14.04 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.27), residues: 879 helix: 2.61 (0.20), residues: 624 sheet: None (None), residues: 0 loop : 0.08 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE E 78 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.948 Fit side-chains REVERT: A 129 ARG cc_start: 0.8780 (tpt90) cc_final: 0.8369 (tpt-90) REVERT: C 73 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7833 (t160) REVERT: D 30 ARG cc_start: 0.7574 (mmt90) cc_final: 0.7074 (mtp180) REVERT: D 31 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7802 (mmmm) REVERT: E 38 PRO cc_start: 0.8280 (Cg_exo) cc_final: 0.8039 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8617 (pm20) cc_final: 0.8238 (pm20) REVERT: E 64 LYS cc_start: 0.8897 (mmtp) cc_final: 0.8476 (mtmt) REVERT: E 120 MET cc_start: 0.8356 (mmt) cc_final: 0.8074 (mtp) REVERT: F 22 LEU cc_start: 0.6867 (mt) cc_final: 0.6539 (mp) REVERT: G 15 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8081 (tttp) outliers start: 14 outliers final: 5 residues processed: 150 average time/residue: 1.9068 time to fit residues: 303.3816 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14074 Z= 0.253 Angle : 0.567 10.648 20215 Z= 0.334 Chirality : 0.034 0.146 2267 Planarity : 0.004 0.046 1542 Dihedral : 30.068 174.822 4236 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 14.83 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.27), residues: 879 helix: 2.62 (0.20), residues: 624 sheet: None (None), residues: 0 loop : 0.09 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.075 Fit side-chains REVERT: A 129 ARG cc_start: 0.8777 (tpt90) cc_final: 0.8368 (tpt-90) REVERT: C 73 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7833 (t160) REVERT: D 30 ARG cc_start: 0.7517 (mmt90) cc_final: 0.7021 (mtp180) REVERT: D 31 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7793 (mmmm) REVERT: E 38 PRO cc_start: 0.8270 (Cg_exo) cc_final: 0.8036 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8614 (pm20) cc_final: 0.8238 (pm20) REVERT: E 64 LYS cc_start: 0.8894 (mmtp) cc_final: 0.8473 (mtmt) REVERT: F 22 LEU cc_start: 0.6872 (mt) cc_final: 0.6555 (mp) REVERT: G 15 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8078 (tttp) outliers start: 9 outliers final: 6 residues processed: 143 average time/residue: 1.7971 time to fit residues: 273.6519 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14074 Z= 0.194 Angle : 0.560 10.640 20215 Z= 0.329 Chirality : 0.033 0.144 2267 Planarity : 0.004 0.040 1542 Dihedral : 30.059 174.810 4236 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 15.22 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.27), residues: 879 helix: 2.69 (0.20), residues: 624 sheet: None (None), residues: 0 loop : 0.12 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.005 0.001 PHE A 67 TYR 0.011 0.001 TYR D 37 ARG 0.012 0.000 ARG L 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.083 Fit side-chains REVERT: A 129 ARG cc_start: 0.8773 (tpt90) cc_final: 0.8365 (tpt-90) REVERT: C 73 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7814 (t160) REVERT: D 30 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7019 (mtp180) REVERT: D 31 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7794 (mmmm) REVERT: E 38 PRO cc_start: 0.8270 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.8232 (pm20) REVERT: E 64 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8478 (mtmt) REVERT: F 22 LEU cc_start: 0.6828 (mt) cc_final: 0.6527 (mp) REVERT: G 15 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8072 (tttp) REVERT: M 428 LYS cc_start: 0.9312 (mtpp) cc_final: 0.9111 (mtmt) outliers start: 9 outliers final: 7 residues processed: 142 average time/residue: 1.8551 time to fit residues: 280.9331 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.0070 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 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 = 0.3523 r_free = 0.3523 target = 0.091612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.066295 restraints weight = 25658.150| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.48 r_work: 0.2884 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14074 Z= 0.243 Angle : 0.561 10.775 20215 Z= 0.330 Chirality : 0.034 0.144 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.014 175.252 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.57 % Allowed : 14.96 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.27), residues: 879 helix: 2.65 (0.20), residues: 624 sheet: None (None), residues: 0 loop : 0.11 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.93 seconds wall clock time: 91 minutes 25.48 seconds (5485.48 seconds total)