Starting phenix.real_space_refine on Sun Dec 10 03:15:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/12_2023/8ox1_17252_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/12_2023/8ox1_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_17252/12_2023/8ox1_17252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/12_2023/8ox1_17252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/12_2023/8ox1_17252_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox1_17252/12_2023/8ox1_17252_updated.pdb" } 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 Residue "A GLU 94": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "M GLU 438": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.31, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 6.60 Conformation dependent library (CDL) restraints added in 1.2 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... running ksdssp... Secondary structure from input PDB file: 41 helices and 0 sheets defined 61.0% alpha, 0.0% beta 140 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 6.96 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 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 86 through 114 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 78 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 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.367A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.597A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 397 removed outlier: 3.761A pdb=" N LEU L 391 " --> pdb=" O GLU L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 403 through 409 Processing helix chain 'L' and resid 417 through 430 Processing helix chain 'M' and resid 385 through 397 Processing helix chain 'M' and resid 403 through 409 Processing helix chain 'M' and resid 417 through 429 385 hydrogen bonds defined for protein. 1104 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: 5.03 Time building geometry restraints manager: 7.05 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: 98.56 - 105.66: 1494 105.66 - 112.77: 7450 112.77 - 119.87: 4988 119.87 - 126.97: 5573 126.97 - 134.07: 710 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: 3482 2.84 - 3.36: 11675 3.36 - 3.87: 26445 3.87 - 4.39: 30857 4.39 - 4.90: 42324 Nonbonded interactions: 114783 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DG J 70 " model vdw 2.326 2.440 nonbonded pdb=" OE2 GLU M 387 " pdb=" N ASN M 413 " model vdw 2.336 2.520 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.349 2.440 nonbonded pdb=" O ARG L 380 " pdb=" NE2 GLN L 381 " model vdw 2.403 2.520 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.418 2.440 ... (remaining 114778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.010 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: 16.200 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 43.040 Find NCS groups from input model: 0.700 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.430 ------------------------------------------------------------------------------- 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= 0.520 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 fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.103 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 1.8714 time to fit residues: 355.0761 Evaluate side-chains 138 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4272 ------------------------------------------------------------------------------- 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: 2.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14074 Z= 0.217 Angle : 0.569 8.627 20215 Z= 0.342 Chirality : 0.034 0.130 2267 Planarity : 0.005 0.040 1542 Dihedral : 29.890 165.737 4236 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.84 % Allowed : 10.10 % Favored : 88.06 % 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: 1.81 (0.27), residues: 879 helix: 1.94 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.54 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 383 HIS 0.003 0.001 HIS E 113 PHE 0.022 0.002 PHE A 104 TYR 0.014 0.001 TYR D 37 ARG 0.005 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 154 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.184 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 143 average time/residue: 1.7516 time to fit residues: 267.4242 Evaluate side-chains 135 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.0010 chunk 102 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14074 Z= 0.171 Angle : 0.545 8.385 20215 Z= 0.329 Chirality : 0.033 0.139 2267 Planarity : 0.004 0.040 1542 Dihedral : 29.891 165.745 4236 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.31 % Allowed : 10.89 % Favored : 87.80 % 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: 2.02 (0.27), residues: 879 helix: 2.04 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.32 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 383 HIS 0.002 0.001 HIS F 75 PHE 0.010 0.001 PHE A 104 TYR 0.010 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 *********************** 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 148 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.166 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 143 average time/residue: 1.7740 time to fit residues: 270.6043 Evaluate side-chains 132 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.4952 time to fit residues: 2.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14074 Z= 0.415 Angle : 0.628 7.089 20215 Z= 0.369 Chirality : 0.040 0.145 2267 Planarity : 0.005 0.039 1542 Dihedral : 30.489 169.085 4236 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.23 % Allowed : 10.24 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.27), residues: 879 helix: 1.87 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 383 HIS 0.005 0.001 HIS E 113 PHE 0.010 0.002 PHE E 78 TYR 0.011 0.002 TYR D 37 ARG 0.006 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 156 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 146 average time/residue: 1.8825 time to fit residues: 292.2171 Evaluate side-chains 141 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 4 average time/residue: 1.1381 time to fit residues: 6.2582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14074 Z= 0.310 Angle : 0.590 8.389 20215 Z= 0.349 Chirality : 0.036 0.145 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.414 169.542 4236 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.10 % Allowed : 11.81 % Favored : 86.09 % 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: 1.75 (0.27), residues: 879 helix: 1.82 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -0.38 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 383 HIS 0.003 0.001 HIS E 113 PHE 0.007 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.013 0.000 ARG L 423 *********************** 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 154 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.036 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 144 average time/residue: 1.8488 time to fit residues: 283.0457 Evaluate side-chains 139 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 1.1274 time to fit residues: 3.7996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14074 Z= 0.190 Angle : 0.570 8.420 20215 Z= 0.338 Chirality : 0.034 0.173 2267 Planarity : 0.004 0.037 1542 Dihedral : 30.351 169.430 4236 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.62 % Allowed : 11.55 % 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: 1.96 (0.27), residues: 879 helix: 1.94 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -0.22 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 383 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.005 0.000 ARG H 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 159 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.246 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 146 average time/residue: 1.8787 time to fit residues: 291.6929 Evaluate side-chains 142 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 1.4813 time to fit residues: 6.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14074 Z= 0.206 Angle : 0.548 7.832 20215 Z= 0.326 Chirality : 0.033 0.140 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.049 169.305 4236 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.31 % Allowed : 13.52 % Favored : 85.17 % 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: 2.13 (0.27), residues: 879 helix: 2.07 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 383 HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.007 0.000 ARG M 415 *********************** 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 148 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.029 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 142 average time/residue: 1.8531 time to fit residues: 280.4875 Evaluate side-chains 139 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 1.8219 time to fit residues: 3.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14074 Z= 0.247 Angle : 0.560 7.647 20215 Z= 0.331 Chirality : 0.034 0.143 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.042 171.077 4236 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.31 % Allowed : 14.17 % Favored : 84.51 % 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: 2.09 (0.27), residues: 879 helix: 2.05 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -0.17 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 383 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.006 0.000 ARG L 423 *********************** 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 151 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 0.989 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 145 average time/residue: 1.7881 time to fit residues: 275.9905 Evaluate side-chains 140 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 1.5104 time to fit residues: 3.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 107 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** L 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2064 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= 0.200 Angle : 0.563 8.086 20215 Z= 0.332 Chirality : 0.033 0.154 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.028 171.388 4236 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.92 % Allowed : 14.96 % 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: 2.14 (0.27), residues: 879 helix: 2.08 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 383 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.019 0.001 TYR L 410 ARG 0.009 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 145 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.100 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 142 average time/residue: 1.8168 time to fit residues: 275.0480 Evaluate side-chains 139 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.8910 time to fit residues: 3.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14074 Z= 0.183 Angle : 0.571 9.259 20215 Z= 0.333 Chirality : 0.033 0.187 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.995 171.512 4236 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.92 % Allowed : 15.09 % 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: 2.19 (0.28), residues: 879 helix: 2.09 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 383 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE L 412 TYR 0.011 0.001 TYR D 37 ARG 0.009 0.000 ARG H 96 ********************** 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 143 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.106 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 140 average time/residue: 1.7659 time to fit residues: 265.2535 Evaluate side-chains 139 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 0.9448 time to fit residues: 3.4850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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: 0.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN L 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065713 restraints weight = 25562.847| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.47 r_work: 0.2870 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14074 Z= 0.268 Angle : 0.578 8.592 20215 Z= 0.338 Chirality : 0.034 0.155 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.038 175.453 4236 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.05 % Allowed : 14.83 % 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: 2.13 (0.27), residues: 879 helix: 2.08 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -0.17 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 385 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE L 412 TYR 0.010 0.001 TYR D 37 ARG 0.010 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5114.63 seconds wall clock time: 90 minutes 54.67 seconds (5454.67 seconds total)