Starting phenix.real_space_refine on Sat Mar 16 07:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/03_2024/8g8b_29845.pdb" } resolution = 4.3 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= 0.003 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 336 5.49 5 S 17 5.16 5 C 7819 2.51 5 N 2611 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14067 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 863 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3419 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3469 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1080 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Time building chain proxies: 8.77, per 1000 atoms: 0.62 Number of scatterers: 14067 At special positions: 0 Unit cell: (80.5, 119.14, 172.27, 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 17 16.00 P 336 15.00 O 3284 8.00 N 2611 7.00 C 7819 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: 7.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 74.5% alpha, 2.4% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.053A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.736A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.233A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 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 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.950A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.363A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 100 through 121 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.552A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 239 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A 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: 6.705A 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: 7.125A 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 101 through 102 removed outlier: 6.758A 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: 6.760A 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: 6.981A 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 78 491 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 7.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2622 1.33 - 1.45: 4963 1.45 - 1.57: 6717 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 15000 Sorted by residual: bond pdb=" N THR E 32 " pdb=" CA THR E 32 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.27e+00 bond pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.86e+00 bond pdb=" C1' DC J -96 " pdb=" N1 DC J -96 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.20e+00 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.88e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.57: 1273 104.57 - 111.94: 8343 111.94 - 119.31: 4624 119.31 - 126.68: 6412 126.68 - 134.05: 1042 Bond angle restraints: 21694 Sorted by residual: angle pdb=" O3' DG J -71 " pdb=" C3' DG J -71 " pdb=" C2' DG J -71 " ideal model delta sigma weight residual 111.50 103.17 8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" O3' DG J -73 " pdb=" C3' DG J -73 " pdb=" C2' DG J -73 " ideal model delta sigma weight residual 111.50 104.37 7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" O3' DA I 78 " pdb=" C3' DA I 78 " pdb=" C2' DA I 78 " ideal model delta sigma weight residual 111.50 104.62 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4' DC I 75 " pdb=" C3' DC I 75 " pdb=" O3' DC I 75 " ideal model delta sigma weight residual 110.00 104.22 5.78 1.50e+00 4.44e-01 1.48e+01 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6500 35.81 - 71.62: 1745 71.62 - 107.42: 15 107.42 - 143.23: 2 143.23 - 179.04: 1 Dihedral angle restraints: 8263 sinusoidal: 5648 harmonic: 2615 Sorted by residual: dihedral pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.04 -179.04 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 82 " pdb=" C3' DA I 82 " pdb=" O3' DA I 82 " pdb=" P DC I 83 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1952 0.041 - 0.083: 438 0.083 - 0.124: 63 0.124 - 0.165: 10 0.165 - 0.206: 5 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C3' DC I 75 " pdb=" C4' DC I 75 " pdb=" O3' DC I 75 " pdb=" C2' DC I 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DT J -76 " pdb=" C4' DT J -76 " pdb=" O3' DT J -76 " pdb=" C2' DT J -76 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C3' DG J -71 " pdb=" C4' DG J -71 " pdb=" O3' DG J -71 " pdb=" C2' DG J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 2465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 79 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 79 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT I 79 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 79 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT I 79 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 79 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 79 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT I 79 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 79 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C GLY F 56 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY F 56 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL F 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO G 80 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 146 2.63 - 3.20: 11304 3.20 - 3.76: 26958 3.76 - 4.33: 36243 4.33 - 4.90: 50059 Nonbonded interactions: 124710 Sorted by model distance: nonbonded pdb=" O2 DC I 85 " pdb=" N2 DG J -85 " model vdw 2.061 2.520 nonbonded pdb=" N6 DA I 72 " pdb=" N3 DT J -72 " model vdw 2.065 2.560 nonbonded pdb=" CD PRO E 30 " pdb=" OE1 GLU X 209 " model vdw 2.132 3.440 nonbonded pdb=" N1 DA I 72 " pdb=" O2 DT J -72 " model vdw 2.152 2.496 nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.276 2.440 ... (remaining 124705 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' and resid 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 2.550 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 46.970 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:2.520 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15000 Z= 0.242 Angle : 0.639 11.794 21694 Z= 0.388 Chirality : 0.036 0.206 2468 Planarity : 0.004 0.044 1582 Dihedral : 28.756 179.040 6571 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 17.15 % Favored : 80.87 % 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: 1.94 (0.27), residues: 882 helix: 1.93 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.002 TYR H 80 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 312 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9228 (mt) cc_final: 0.8846 (tp) REVERT: A 89 VAL cc_start: 0.9748 (t) cc_final: 0.9395 (m) REVERT: A 90 MET cc_start: 0.9569 (mmp) cc_final: 0.9326 (mmm) REVERT: A 99 TYR cc_start: 0.8162 (t80) cc_final: 0.7841 (t80) REVERT: A 106 ASP cc_start: 0.9386 (m-30) cc_final: 0.8954 (t0) REVERT: A 110 CYS cc_start: 0.9719 (m) cc_final: 0.9434 (m) REVERT: B 53 GLU cc_start: 0.9278 (tp30) cc_final: 0.8811 (tt0) REVERT: B 59 LYS cc_start: 0.9633 (tppp) cc_final: 0.9388 (tppp) REVERT: B 61 PHE cc_start: 0.9349 (t80) cc_final: 0.8959 (t80) REVERT: B 66 ILE cc_start: 0.9625 (mt) cc_final: 0.9422 (tt) REVERT: C 51 LEU cc_start: 0.9717 (tp) cc_final: 0.9504 (tp) REVERT: C 75 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8343 (mmmt) REVERT: C 94 ASN cc_start: 0.9568 (t0) cc_final: 0.9177 (m-40) REVERT: C 101 THR cc_start: 0.9445 (m) cc_final: 0.9047 (t) REVERT: D 34 TYR cc_start: 0.9188 (m-80) cc_final: 0.8727 (m-80) REVERT: D 64 ASN cc_start: 0.9598 (m-40) cc_final: 0.8956 (m110) REVERT: E 65 LEU cc_start: 0.9858 (mt) cc_final: 0.9618 (mt) REVERT: E 94 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8919 (tp30) REVERT: E 109 LEU cc_start: 0.9672 (mt) cc_final: 0.9301 (mt) REVERT: F 26 ILE cc_start: 0.9212 (tp) cc_final: 0.8951 (tp) REVERT: F 46 ILE cc_start: 0.9314 (mt) cc_final: 0.8878 (tp) REVERT: F 51 TYR cc_start: 0.8809 (m-80) cc_final: 0.8470 (m-80) REVERT: F 53 GLU cc_start: 0.9195 (tp30) cc_final: 0.8912 (tt0) REVERT: F 64 ASN cc_start: 0.9661 (m-40) cc_final: 0.9248 (m-40) REVERT: F 74 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9102 (mt-10) REVERT: G 25 PHE cc_start: 0.8966 (m-80) cc_final: 0.8594 (m-10) REVERT: G 51 LEU cc_start: 0.9900 (tp) cc_final: 0.9654 (tp) REVERT: G 56 GLU cc_start: 0.8697 (tt0) cc_final: 0.7532 (tt0) REVERT: G 73 ASN cc_start: 0.9480 (m110) cc_final: 0.9070 (m110) REVERT: G 93 LEU cc_start: 0.9811 (mt) cc_final: 0.9580 (tp) REVERT: G 94 ASN cc_start: 0.9749 (t0) cc_final: 0.9359 (m-40) REVERT: G 101 THR cc_start: 0.9441 (m) cc_final: 0.9144 (p) REVERT: H 34 TYR cc_start: 0.9144 (m-80) cc_final: 0.8306 (m-10) REVERT: H 41 VAL cc_start: 0.9742 (t) cc_final: 0.9493 (p) REVERT: H 58 ILE cc_start: 0.9776 (mt) cc_final: 0.9432 (mt) REVERT: H 59 MET cc_start: 0.9744 (mmm) cc_final: 0.9533 (mmm) REVERT: H 64 ASN cc_start: 0.9453 (m-40) cc_final: 0.9223 (m110) REVERT: H 76 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9298 (ptp-110) REVERT: H 90 GLU cc_start: 0.9535 (mp0) cc_final: 0.9034 (mp0) REVERT: H 98 LEU cc_start: 0.8787 (mt) cc_final: 0.8338 (mt) REVERT: H 109 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (p) outliers start: 15 outliers final: 2 residues processed: 323 average time/residue: 0.3425 time to fit residues: 146.6690 Evaluate side-chains 187 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15000 Z= 0.296 Angle : 0.676 12.703 21694 Z= 0.396 Chirality : 0.037 0.194 2468 Planarity : 0.007 0.166 1582 Dihedral : 31.430 177.865 4762 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 1.94 (0.27), residues: 882 helix: 1.83 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 207 HIS 0.010 0.002 HIS F 75 PHE 0.021 0.002 PHE X 278 TYR 0.028 0.003 TYR H 80 ARG 0.011 0.001 ARG X 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9697 (mp) cc_final: 0.9456 (mt) REVERT: A 90 MET cc_start: 0.9720 (mmp) cc_final: 0.9460 (mmp) REVERT: A 92 LEU cc_start: 0.9833 (mt) cc_final: 0.9600 (mp) REVERT: A 106 ASP cc_start: 0.9408 (m-30) cc_final: 0.9168 (t0) REVERT: A 126 LEU cc_start: 0.9550 (mm) cc_final: 0.9274 (tp) REVERT: B 53 GLU cc_start: 0.9385 (tp30) cc_final: 0.9059 (tt0) REVERT: B 59 LYS cc_start: 0.9705 (tppp) cc_final: 0.9403 (tppt) REVERT: B 66 ILE cc_start: 0.9681 (mt) cc_final: 0.9408 (tt) REVERT: B 97 LEU cc_start: 0.9307 (tp) cc_final: 0.8834 (tp) REVERT: C 25 PHE cc_start: 0.8500 (m-10) cc_final: 0.8187 (m-80) REVERT: C 94 ASN cc_start: 0.9612 (t0) cc_final: 0.9197 (t0) REVERT: C 101 THR cc_start: 0.9392 (m) cc_final: 0.9020 (t) REVERT: D 31 LYS cc_start: 0.9707 (tppp) cc_final: 0.9495 (mmtt) REVERT: D 59 MET cc_start: 0.9851 (mmm) cc_final: 0.9446 (mmm) REVERT: D 64 ASN cc_start: 0.9598 (m-40) cc_final: 0.9232 (m-40) REVERT: D 79 HIS cc_start: 0.9750 (t-90) cc_final: 0.9530 (t-90) REVERT: E 50 GLU cc_start: 0.9734 (mt-10) cc_final: 0.9454 (mt-10) REVERT: E 74 ILE cc_start: 0.9707 (mt) cc_final: 0.9396 (mt) REVERT: E 94 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9026 (mm-30) REVERT: F 53 GLU cc_start: 0.9561 (tp30) cc_final: 0.9233 (tt0) REVERT: F 57 VAL cc_start: 0.9676 (t) cc_final: 0.9454 (p) REVERT: F 96 THR cc_start: 0.9500 (p) cc_final: 0.9281 (t) REVERT: F 100 PHE cc_start: 0.8302 (m-80) cc_final: 0.7999 (m-80) REVERT: G 25 PHE cc_start: 0.9238 (m-80) cc_final: 0.9029 (m-10) REVERT: G 73 ASN cc_start: 0.9273 (m110) cc_final: 0.8929 (m110) REVERT: G 90 ASP cc_start: 0.9058 (t0) cc_final: 0.8641 (t70) REVERT: G 94 ASN cc_start: 0.9747 (t0) cc_final: 0.9369 (t0) REVERT: G 101 THR cc_start: 0.9249 (m) cc_final: 0.8855 (p) REVERT: H 34 TYR cc_start: 0.9540 (m-80) cc_final: 0.8906 (m-80) REVERT: H 59 MET cc_start: 0.9753 (mmm) cc_final: 0.9540 (mmp) REVERT: H 73 GLU cc_start: 0.9433 (tp30) cc_final: 0.8578 (tp30) REVERT: H 76 ARG cc_start: 0.9623 (mtm-85) cc_final: 0.9358 (ptp-110) REVERT: H 79 HIS cc_start: 0.9562 (t-90) cc_final: 0.9331 (t-90) REVERT: H 90 GLU cc_start: 0.9357 (mp0) cc_final: 0.8965 (mp0) REVERT: H 97 LEU cc_start: 0.9258 (mt) cc_final: 0.9025 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3229 time to fit residues: 101.4059 Evaluate side-chains 167 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15000 Z= 0.318 Angle : 0.658 11.796 21694 Z= 0.388 Chirality : 0.036 0.145 2468 Planarity : 0.005 0.042 1582 Dihedral : 32.068 177.660 4762 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 1.78 (0.27), residues: 882 helix: 1.69 (0.19), residues: 661 sheet: None (None), residues: 0 loop : -0.27 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 PHE 0.024 0.002 PHE F 61 TYR 0.028 0.002 TYR B 88 ARG 0.007 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9228 (mt-10) REVERT: A 81 ASP cc_start: 0.8845 (m-30) cc_final: 0.8575 (m-30) REVERT: A 90 MET cc_start: 0.9760 (mmp) cc_final: 0.9512 (mmp) REVERT: A 126 LEU cc_start: 0.9586 (mm) cc_final: 0.9310 (tp) REVERT: B 59 LYS cc_start: 0.9715 (tppp) cc_final: 0.9339 (tppt) REVERT: B 97 LEU cc_start: 0.9345 (tp) cc_final: 0.8844 (tp) REVERT: C 25 PHE cc_start: 0.8214 (m-10) cc_final: 0.7991 (m-10) REVERT: C 83 LEU cc_start: 0.9775 (mp) cc_final: 0.9347 (mp) REVERT: C 90 ASP cc_start: 0.8687 (t0) cc_final: 0.8430 (t70) REVERT: C 94 ASN cc_start: 0.9558 (t0) cc_final: 0.9185 (t0) REVERT: C 101 THR cc_start: 0.9252 (m) cc_final: 0.8955 (p) REVERT: D 58 ILE cc_start: 0.9813 (mt) cc_final: 0.9555 (mt) REVERT: D 59 MET cc_start: 0.9841 (mmm) cc_final: 0.9210 (mmm) REVERT: D 64 ASN cc_start: 0.9452 (m-40) cc_final: 0.9131 (m-40) REVERT: D 65 ASP cc_start: 0.9698 (t0) cc_final: 0.9344 (t0) REVERT: D 79 HIS cc_start: 0.9742 (t-90) cc_final: 0.9504 (t-90) REVERT: D 90 GLU cc_start: 0.9051 (mp0) cc_final: 0.8787 (mp0) REVERT: E 50 GLU cc_start: 0.9721 (mt-10) cc_final: 0.9424 (mt-10) REVERT: E 90 MET cc_start: 0.9537 (ttp) cc_final: 0.9293 (ttp) REVERT: E 94 GLU cc_start: 0.9477 (mm-30) cc_final: 0.8932 (tp30) REVERT: E 99 TYR cc_start: 0.9368 (t80) cc_final: 0.9138 (t80) REVERT: F 53 GLU cc_start: 0.9636 (tp30) cc_final: 0.9279 (tt0) REVERT: F 96 THR cc_start: 0.9340 (p) cc_final: 0.9010 (t) REVERT: F 100 PHE cc_start: 0.8646 (m-80) cc_final: 0.8434 (m-80) REVERT: G 25 PHE cc_start: 0.9153 (m-10) cc_final: 0.8653 (m-10) REVERT: G 73 ASN cc_start: 0.9164 (m110) cc_final: 0.8787 (m110) REVERT: G 94 ASN cc_start: 0.9701 (t0) cc_final: 0.9349 (t0) REVERT: G 101 THR cc_start: 0.9170 (m) cc_final: 0.8711 (p) REVERT: H 34 TYR cc_start: 0.9501 (m-80) cc_final: 0.8839 (m-80) REVERT: H 59 MET cc_start: 0.9811 (mmm) cc_final: 0.9567 (mmm) REVERT: H 73 GLU cc_start: 0.9433 (tp30) cc_final: 0.8750 (tp30) REVERT: H 79 HIS cc_start: 0.9548 (t-90) cc_final: 0.9309 (t-90) REVERT: H 90 GLU cc_start: 0.9319 (mp0) cc_final: 0.8999 (mp0) REVERT: H 117 LYS cc_start: 0.9709 (ptpp) cc_final: 0.9470 (ptmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3114 time to fit residues: 87.7077 Evaluate side-chains 148 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15000 Z= 0.241 Angle : 0.628 12.333 21694 Z= 0.369 Chirality : 0.035 0.149 2468 Planarity : 0.005 0.082 1582 Dihedral : 31.891 176.454 4762 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 882 helix: 1.60 (0.20), residues: 663 sheet: None (None), residues: 0 loop : 0.01 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 207 HIS 0.006 0.001 HIS H 106 PHE 0.013 0.002 PHE A 67 TYR 0.018 0.002 TYR F 51 ARG 0.003 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9283 (mt-10) REVERT: A 81 ASP cc_start: 0.8931 (m-30) cc_final: 0.8658 (m-30) REVERT: A 120 MET cc_start: 0.9416 (tpt) cc_final: 0.8989 (tpp) REVERT: A 126 LEU cc_start: 0.9580 (mm) cc_final: 0.9303 (tp) REVERT: B 59 LYS cc_start: 0.9696 (tppp) cc_final: 0.9224 (tppt) REVERT: B 63 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9116 (mt-10) REVERT: B 88 TYR cc_start: 0.9392 (m-10) cc_final: 0.9136 (m-10) REVERT: B 97 LEU cc_start: 0.9369 (tp) cc_final: 0.8812 (tp) REVERT: C 25 PHE cc_start: 0.8155 (m-10) cc_final: 0.7898 (m-10) REVERT: C 39 TYR cc_start: 0.9193 (m-10) cc_final: 0.8955 (m-80) REVERT: C 83 LEU cc_start: 0.9772 (mp) cc_final: 0.9395 (mp) REVERT: C 90 ASP cc_start: 0.8764 (t0) cc_final: 0.8489 (t70) REVERT: C 94 ASN cc_start: 0.9586 (t0) cc_final: 0.9262 (t0) REVERT: C 101 THR cc_start: 0.9336 (m) cc_final: 0.9032 (p) REVERT: D 34 TYR cc_start: 0.9697 (m-80) cc_final: 0.8954 (m-80) REVERT: D 58 ILE cc_start: 0.9817 (mt) cc_final: 0.9564 (mt) REVERT: D 59 MET cc_start: 0.9805 (mmm) cc_final: 0.9464 (mmm) REVERT: D 64 ASN cc_start: 0.9424 (m-40) cc_final: 0.8734 (m-40) REVERT: D 65 ASP cc_start: 0.9654 (t0) cc_final: 0.9433 (t0) REVERT: D 79 HIS cc_start: 0.9736 (t-90) cc_final: 0.9516 (t-90) REVERT: D 90 GLU cc_start: 0.9026 (mp0) cc_final: 0.8726 (mp0) REVERT: D 98 LEU cc_start: 0.9243 (mm) cc_final: 0.8986 (mm) REVERT: D 103 LEU cc_start: 0.9597 (mt) cc_final: 0.9381 (mt) REVERT: E 50 GLU cc_start: 0.9715 (mt-10) cc_final: 0.9394 (mt-10) REVERT: E 90 MET cc_start: 0.9527 (ttp) cc_final: 0.9273 (ttp) REVERT: E 94 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8779 (tp30) REVERT: E 124 ILE cc_start: 0.9824 (mt) cc_final: 0.9616 (mt) REVERT: F 96 THR cc_start: 0.9333 (p) cc_final: 0.9048 (t) REVERT: F 100 PHE cc_start: 0.8604 (m-80) cc_final: 0.8285 (m-80) REVERT: G 25 PHE cc_start: 0.9053 (m-10) cc_final: 0.8258 (m-10) REVERT: G 64 GLU cc_start: 0.9170 (tp30) cc_final: 0.8790 (tp30) REVERT: G 73 ASN cc_start: 0.9091 (m110) cc_final: 0.8738 (m110) REVERT: G 94 ASN cc_start: 0.9673 (t0) cc_final: 0.9388 (t0) REVERT: G 101 THR cc_start: 0.9159 (m) cc_final: 0.8664 (p) REVERT: H 34 TYR cc_start: 0.9480 (m-80) cc_final: 0.8991 (m-80) REVERT: H 59 MET cc_start: 0.9768 (mmm) cc_final: 0.9546 (mmm) REVERT: H 69 ARG cc_start: 0.9566 (mtm-85) cc_final: 0.9127 (tpt170) REVERT: H 73 GLU cc_start: 0.9333 (tp30) cc_final: 0.8613 (tp30) REVERT: H 76 ARG cc_start: 0.9609 (ptp-110) cc_final: 0.9081 (mtm-85) REVERT: H 79 HIS cc_start: 0.9544 (t-90) cc_final: 0.9259 (t-90) REVERT: H 90 GLU cc_start: 0.9287 (mp0) cc_final: 0.8964 (mp0) REVERT: H 98 LEU cc_start: 0.9463 (tp) cc_final: 0.8091 (tp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3128 time to fit residues: 83.3317 Evaluate side-chains 151 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15000 Z= 0.305 Angle : 0.659 14.391 21694 Z= 0.388 Chirality : 0.036 0.147 2468 Planarity : 0.005 0.046 1582 Dihedral : 32.227 176.989 4762 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 1.51 (0.27), residues: 882 helix: 1.39 (0.20), residues: 662 sheet: None (None), residues: 0 loop : 0.02 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 207 HIS 0.004 0.001 HIS B 75 PHE 0.022 0.002 PHE F 61 TYR 0.025 0.002 TYR H 80 ARG 0.005 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9210 (mt-10) REVERT: A 81 ASP cc_start: 0.9006 (m-30) cc_final: 0.8743 (m-30) REVERT: A 105 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8459 (tm-30) REVERT: A 109 LEU cc_start: 0.9502 (mt) cc_final: 0.9067 (mt) REVERT: A 126 LEU cc_start: 0.9618 (mm) cc_final: 0.9382 (tt) REVERT: B 44 LYS cc_start: 0.8956 (tttt) cc_final: 0.8704 (ttmm) REVERT: B 59 LYS cc_start: 0.9715 (tppp) cc_final: 0.9285 (tppt) REVERT: B 63 GLU cc_start: 0.9710 (mt-10) cc_final: 0.9232 (mt-10) REVERT: B 81 VAL cc_start: 0.9495 (t) cc_final: 0.9245 (p) REVERT: C 25 PHE cc_start: 0.8222 (m-10) cc_final: 0.7816 (m-10) REVERT: C 83 LEU cc_start: 0.9773 (mp) cc_final: 0.9409 (mp) REVERT: C 90 ASP cc_start: 0.8746 (t0) cc_final: 0.8466 (t70) REVERT: C 94 ASN cc_start: 0.9613 (t0) cc_final: 0.9247 (t0) REVERT: C 101 THR cc_start: 0.9342 (m) cc_final: 0.8980 (p) REVERT: D 34 TYR cc_start: 0.9644 (m-80) cc_final: 0.8922 (m-80) REVERT: D 58 ILE cc_start: 0.9832 (mt) cc_final: 0.9597 (mt) REVERT: D 59 MET cc_start: 0.9823 (mmm) cc_final: 0.9463 (mmm) REVERT: D 64 ASN cc_start: 0.9478 (m-40) cc_final: 0.8919 (m-40) REVERT: D 67 PHE cc_start: 0.9715 (t80) cc_final: 0.9505 (t80) REVERT: D 79 HIS cc_start: 0.9709 (t-90) cc_final: 0.9368 (t-90) REVERT: D 98 LEU cc_start: 0.9264 (mm) cc_final: 0.8722 (mm) REVERT: D 103 LEU cc_start: 0.9645 (mt) cc_final: 0.9416 (mt) REVERT: E 50 GLU cc_start: 0.9712 (mt-10) cc_final: 0.9434 (mt-10) REVERT: E 90 MET cc_start: 0.9570 (ttp) cc_final: 0.9341 (ptm) REVERT: G 25 PHE cc_start: 0.9089 (m-10) cc_final: 0.8458 (m-10) REVERT: G 64 GLU cc_start: 0.9164 (tp30) cc_final: 0.8771 (tp30) REVERT: G 73 ASN cc_start: 0.9114 (m110) cc_final: 0.8797 (m110) REVERT: G 94 ASN cc_start: 0.9668 (t0) cc_final: 0.9343 (t0) REVERT: H 34 TYR cc_start: 0.9506 (m-80) cc_final: 0.9186 (m-80) REVERT: H 59 MET cc_start: 0.9777 (mmm) cc_final: 0.9511 (mmm) REVERT: H 64 ASN cc_start: 0.9595 (m110) cc_final: 0.9326 (m110) REVERT: H 73 GLU cc_start: 0.9371 (tp30) cc_final: 0.9042 (tp30) REVERT: H 76 ARG cc_start: 0.9494 (ptp-110) cc_final: 0.9201 (mtm-85) REVERT: H 122 LYS cc_start: 0.8931 (tmmt) cc_final: 0.8655 (tmmt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3227 time to fit residues: 79.3481 Evaluate side-chains 132 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 37 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15000 Z= 0.273 Angle : 0.658 15.831 21694 Z= 0.384 Chirality : 0.036 0.148 2468 Planarity : 0.005 0.053 1582 Dihedral : 32.222 176.603 4762 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.13 % Allowed : 1.85 % Favored : 98.02 % 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: 1.48 (0.27), residues: 882 helix: 1.36 (0.20), residues: 660 sheet: None (None), residues: 0 loop : 0.03 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP X 207 HIS 0.004 0.001 HIS B 75 PHE 0.016 0.002 PHE A 67 TYR 0.018 0.002 TYR E 99 ARG 0.009 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9286 (mt-10) REVERT: A 81 ASP cc_start: 0.8810 (m-30) cc_final: 0.8600 (m-30) REVERT: A 90 MET cc_start: 0.9724 (mmp) cc_final: 0.9491 (mmp) REVERT: A 97 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8842 (mt-10) REVERT: A 105 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 109 LEU cc_start: 0.9507 (mt) cc_final: 0.9064 (mt) REVERT: A 120 MET cc_start: 0.9348 (tpt) cc_final: 0.8907 (tpp) REVERT: A 126 LEU cc_start: 0.9619 (mm) cc_final: 0.9416 (tt) REVERT: B 59 LYS cc_start: 0.9689 (tppp) cc_final: 0.9240 (tppt) REVERT: B 63 GLU cc_start: 0.9666 (mt-10) cc_final: 0.9165 (mt-10) REVERT: B 81 VAL cc_start: 0.9371 (t) cc_final: 0.9097 (p) REVERT: B 97 LEU cc_start: 0.9407 (tp) cc_final: 0.9147 (tp) REVERT: B 98 TYR cc_start: 0.8476 (m-10) cc_final: 0.8025 (m-80) REVERT: C 25 PHE cc_start: 0.8532 (m-10) cc_final: 0.8163 (m-10) REVERT: C 83 LEU cc_start: 0.9782 (mp) cc_final: 0.9458 (mp) REVERT: C 90 ASP cc_start: 0.8840 (t0) cc_final: 0.8552 (t70) REVERT: C 94 ASN cc_start: 0.9630 (t0) cc_final: 0.9265 (t0) REVERT: C 101 THR cc_start: 0.9433 (m) cc_final: 0.9088 (p) REVERT: D 34 TYR cc_start: 0.9616 (m-80) cc_final: 0.8919 (m-80) REVERT: D 59 MET cc_start: 0.9811 (mmm) cc_final: 0.9555 (mmm) REVERT: D 64 ASN cc_start: 0.9464 (m-40) cc_final: 0.8931 (m-40) REVERT: D 65 ASP cc_start: 0.9596 (t70) cc_final: 0.9098 (t0) REVERT: D 79 HIS cc_start: 0.9696 (t-90) cc_final: 0.9355 (t-90) REVERT: D 98 LEU cc_start: 0.9361 (mm) cc_final: 0.8998 (mm) REVERT: D 103 LEU cc_start: 0.9558 (mt) cc_final: 0.9311 (mt) REVERT: E 50 GLU cc_start: 0.9733 (mt-10) cc_final: 0.9487 (mt-10) REVERT: E 90 MET cc_start: 0.9581 (ttp) cc_final: 0.9272 (ttp) REVERT: E 99 TYR cc_start: 0.9521 (t80) cc_final: 0.9204 (t80) REVERT: G 25 PHE cc_start: 0.9041 (m-10) cc_final: 0.8101 (m-10) REVERT: G 56 GLU cc_start: 0.8890 (tt0) cc_final: 0.6662 (tt0) REVERT: G 94 ASN cc_start: 0.9668 (t0) cc_final: 0.9379 (t0) REVERT: G 101 THR cc_start: 0.9445 (m) cc_final: 0.9090 (p) REVERT: H 34 TYR cc_start: 0.9495 (m-80) cc_final: 0.9290 (m-80) REVERT: H 59 MET cc_start: 0.9760 (mmm) cc_final: 0.9531 (mmm) REVERT: H 64 ASN cc_start: 0.9619 (m110) cc_final: 0.9410 (m-40) REVERT: H 69 ARG cc_start: 0.9557 (mtm-85) cc_final: 0.9240 (tpt90) REVERT: H 70 ILE cc_start: 0.9841 (mm) cc_final: 0.9512 (mm) REVERT: H 73 GLU cc_start: 0.9356 (tp30) cc_final: 0.9077 (tm-30) REVERT: H 90 GLU cc_start: 0.9063 (mp0) cc_final: 0.8859 (mp0) REVERT: H 98 LEU cc_start: 0.9561 (tp) cc_final: 0.7992 (tp) REVERT: H 110 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8715 (mm-30) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.3179 time to fit residues: 75.0519 Evaluate side-chains 126 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 50.0000 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15000 Z= 0.235 Angle : 0.629 11.896 21694 Z= 0.370 Chirality : 0.035 0.181 2468 Planarity : 0.004 0.044 1582 Dihedral : 31.995 176.339 4762 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.58 (0.27), residues: 882 helix: 1.43 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.08 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 207 HIS 0.011 0.002 HIS F 75 PHE 0.015 0.002 PHE A 67 TYR 0.017 0.002 TYR G 50 ARG 0.004 0.000 ARG X 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9343 (mt-10) REVERT: A 81 ASP cc_start: 0.8811 (m-30) cc_final: 0.8592 (m-30) REVERT: A 90 MET cc_start: 0.9722 (mmp) cc_final: 0.9484 (mmp) REVERT: A 97 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8893 (mt-10) REVERT: A 105 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 109 LEU cc_start: 0.9521 (mt) cc_final: 0.9066 (mt) REVERT: A 126 LEU cc_start: 0.9608 (mm) cc_final: 0.9381 (tt) REVERT: B 63 GLU cc_start: 0.9650 (mt-10) cc_final: 0.8964 (tp30) REVERT: B 81 VAL cc_start: 0.9511 (t) cc_final: 0.9286 (p) REVERT: B 97 LEU cc_start: 0.9422 (tp) cc_final: 0.9094 (tp) REVERT: C 25 PHE cc_start: 0.8485 (m-10) cc_final: 0.8142 (m-10) REVERT: C 83 LEU cc_start: 0.9787 (mp) cc_final: 0.9418 (mp) REVERT: C 90 ASP cc_start: 0.8959 (t0) cc_final: 0.8720 (t70) REVERT: C 94 ASN cc_start: 0.9604 (t0) cc_final: 0.9255 (t0) REVERT: C 101 THR cc_start: 0.9421 (m) cc_final: 0.9128 (p) REVERT: C 112 GLN cc_start: 0.9574 (tp40) cc_final: 0.9162 (tp-100) REVERT: D 34 TYR cc_start: 0.9597 (m-80) cc_final: 0.8909 (m-80) REVERT: D 56 MET cc_start: 0.9552 (tpt) cc_final: 0.9311 (tpt) REVERT: D 59 MET cc_start: 0.9804 (mmm) cc_final: 0.9465 (mmm) REVERT: D 63 VAL cc_start: 0.9649 (t) cc_final: 0.9420 (p) REVERT: D 64 ASN cc_start: 0.9429 (m110) cc_final: 0.8954 (m110) REVERT: D 67 PHE cc_start: 0.9664 (t80) cc_final: 0.9455 (t80) REVERT: D 79 HIS cc_start: 0.9678 (t-90) cc_final: 0.9322 (t-90) REVERT: D 90 GLU cc_start: 0.8988 (mp0) cc_final: 0.8778 (mp0) REVERT: D 98 LEU cc_start: 0.9438 (mm) cc_final: 0.9095 (mm) REVERT: E 46 VAL cc_start: 0.9642 (t) cc_final: 0.9416 (t) REVERT: E 50 GLU cc_start: 0.9730 (mt-10) cc_final: 0.9497 (mt-10) REVERT: E 90 MET cc_start: 0.9541 (ttp) cc_final: 0.9236 (ttp) REVERT: E 99 TYR cc_start: 0.9481 (t80) cc_final: 0.9220 (t80) REVERT: F 68 ASP cc_start: 0.9410 (m-30) cc_final: 0.9208 (m-30) REVERT: F 72 TYR cc_start: 0.9042 (m-80) cc_final: 0.8563 (m-80) REVERT: G 25 PHE cc_start: 0.9021 (m-10) cc_final: 0.7908 (m-10) REVERT: G 56 GLU cc_start: 0.8973 (tt0) cc_final: 0.6711 (tt0) REVERT: G 94 ASN cc_start: 0.9615 (t0) cc_final: 0.9302 (t0) REVERT: G 101 THR cc_start: 0.9416 (m) cc_final: 0.9045 (p) REVERT: H 34 TYR cc_start: 0.9440 (m-80) cc_final: 0.9091 (m-80) REVERT: H 59 MET cc_start: 0.9717 (mmm) cc_final: 0.9431 (mmm) REVERT: H 64 ASN cc_start: 0.9594 (m110) cc_final: 0.9310 (m110) REVERT: H 69 ARG cc_start: 0.9565 (mtm-85) cc_final: 0.9175 (tpt90) REVERT: H 73 GLU cc_start: 0.9292 (tp30) cc_final: 0.9042 (tp30) REVERT: H 76 ARG cc_start: 0.9574 (ptp-110) cc_final: 0.9166 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3129 time to fit residues: 77.0841 Evaluate side-chains 136 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.7415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15000 Z= 0.215 Angle : 0.623 11.424 21694 Z= 0.365 Chirality : 0.034 0.148 2468 Planarity : 0.004 0.047 1582 Dihedral : 31.827 176.532 4762 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.65 (0.28), residues: 882 helix: 1.48 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 207 HIS 0.009 0.001 HIS F 75 PHE 0.015 0.002 PHE A 67 TYR 0.042 0.002 TYR H 37 ARG 0.007 0.000 ARG X 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9591 (mt-10) cc_final: 0.9335 (mt-10) REVERT: A 90 MET cc_start: 0.9704 (mmp) cc_final: 0.9480 (mmp) REVERT: A 105 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 109 LEU cc_start: 0.9525 (mt) cc_final: 0.9071 (mt) REVERT: A 120 MET cc_start: 0.9383 (tpt) cc_final: 0.9122 (tpp) REVERT: A 126 LEU cc_start: 0.9599 (mm) cc_final: 0.9380 (tt) REVERT: B 63 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9035 (mt-10) REVERT: B 97 LEU cc_start: 0.9398 (tp) cc_final: 0.9068 (tp) REVERT: B 100 PHE cc_start: 0.7768 (m-10) cc_final: 0.7207 (m-10) REVERT: C 25 PHE cc_start: 0.8545 (m-10) cc_final: 0.8137 (m-10) REVERT: C 90 ASP cc_start: 0.8707 (t0) cc_final: 0.8411 (t70) REVERT: C 94 ASN cc_start: 0.9602 (t0) cc_final: 0.9276 (t0) REVERT: C 101 THR cc_start: 0.9371 (m) cc_final: 0.9096 (p) REVERT: D 34 TYR cc_start: 0.9495 (m-80) cc_final: 0.8796 (m-80) REVERT: D 59 MET cc_start: 0.9812 (mmm) cc_final: 0.9410 (mmm) REVERT: D 64 ASN cc_start: 0.9390 (m110) cc_final: 0.8944 (m110) REVERT: D 65 ASP cc_start: 0.9658 (t0) cc_final: 0.8846 (t0) REVERT: D 67 PHE cc_start: 0.9622 (t80) cc_final: 0.9355 (t80) REVERT: D 69 ARG cc_start: 0.9411 (ptp-110) cc_final: 0.8711 (ptm160) REVERT: D 79 HIS cc_start: 0.9657 (t-90) cc_final: 0.9431 (t-90) REVERT: D 90 GLU cc_start: 0.8974 (mp0) cc_final: 0.8751 (mp0) REVERT: D 98 LEU cc_start: 0.9410 (mm) cc_final: 0.8863 (mm) REVERT: E 46 VAL cc_start: 0.9644 (t) cc_final: 0.9418 (t) REVERT: E 50 GLU cc_start: 0.9731 (mt-10) cc_final: 0.9493 (mt-10) REVERT: E 90 MET cc_start: 0.9526 (ttp) cc_final: 0.9232 (ttp) REVERT: E 99 TYR cc_start: 0.9475 (t80) cc_final: 0.9203 (t80) REVERT: F 72 TYR cc_start: 0.9032 (m-80) cc_final: 0.8661 (m-80) REVERT: G 25 PHE cc_start: 0.8728 (m-10) cc_final: 0.7769 (m-10) REVERT: G 56 GLU cc_start: 0.8887 (tt0) cc_final: 0.6753 (tt0) REVERT: G 94 ASN cc_start: 0.9591 (t0) cc_final: 0.9306 (t0) REVERT: G 101 THR cc_start: 0.9286 (m) cc_final: 0.8909 (p) REVERT: H 34 TYR cc_start: 0.9443 (m-80) cc_final: 0.9221 (m-80) REVERT: H 64 ASN cc_start: 0.9608 (m110) cc_final: 0.9366 (m-40) REVERT: H 73 GLU cc_start: 0.9328 (tp30) cc_final: 0.9114 (tp30) REVERT: H 98 LEU cc_start: 0.9444 (tp) cc_final: 0.7840 (tp) REVERT: H 110 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8826 (mm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3300 time to fit residues: 81.3730 Evaluate side-chains 132 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15000 Z= 0.301 Angle : 0.672 13.053 21694 Z= 0.390 Chirality : 0.036 0.180 2468 Planarity : 0.005 0.046 1582 Dihedral : 32.147 177.282 4762 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.52 (0.28), residues: 882 helix: 1.38 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 207 HIS 0.009 0.001 HIS F 75 PHE 0.022 0.002 PHE B 61 TYR 0.035 0.002 TYR H 37 ARG 0.017 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9344 (mt-10) REVERT: A 81 ASP cc_start: 0.8812 (m-30) cc_final: 0.8503 (m-30) REVERT: A 90 MET cc_start: 0.9732 (mmp) cc_final: 0.9502 (mmm) REVERT: A 105 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 109 LEU cc_start: 0.9526 (mt) cc_final: 0.9085 (mt) REVERT: A 120 MET cc_start: 0.9337 (tpt) cc_final: 0.8916 (tpp) REVERT: A 126 LEU cc_start: 0.9619 (mm) cc_final: 0.9407 (tt) REVERT: B 63 GLU cc_start: 0.9571 (mt-10) cc_final: 0.9123 (mt-10) REVERT: B 72 TYR cc_start: 0.8984 (m-10) cc_final: 0.8677 (m-10) REVERT: B 96 THR cc_start: 0.8679 (m) cc_final: 0.8227 (m) REVERT: B 97 LEU cc_start: 0.9418 (tp) cc_final: 0.9097 (tp) REVERT: C 25 PHE cc_start: 0.7946 (m-10) cc_final: 0.7616 (m-10) REVERT: C 83 LEU cc_start: 0.9800 (mp) cc_final: 0.9429 (mp) REVERT: C 94 ASN cc_start: 0.9488 (t0) cc_final: 0.9125 (t0) REVERT: C 101 THR cc_start: 0.9385 (m) cc_final: 0.9069 (p) REVERT: D 34 TYR cc_start: 0.9545 (m-80) cc_final: 0.8869 (m-80) REVERT: D 56 MET cc_start: 0.9489 (tpt) cc_final: 0.9225 (tpt) REVERT: D 59 MET cc_start: 0.9828 (mmm) cc_final: 0.9501 (mmm) REVERT: D 64 ASN cc_start: 0.9351 (m110) cc_final: 0.8977 (m110) REVERT: D 67 PHE cc_start: 0.9610 (t80) cc_final: 0.9277 (t80) REVERT: D 79 HIS cc_start: 0.9633 (t-90) cc_final: 0.9269 (t-90) REVERT: D 98 LEU cc_start: 0.9474 (mm) cc_final: 0.8950 (mm) REVERT: E 50 GLU cc_start: 0.9730 (mt-10) cc_final: 0.9513 (mt-10) REVERT: E 68 GLN cc_start: 0.9360 (pp30) cc_final: 0.9122 (pp30) REVERT: E 90 MET cc_start: 0.9599 (ttp) cc_final: 0.9305 (ttp) REVERT: E 99 TYR cc_start: 0.9421 (t80) cc_final: 0.9149 (t80) REVERT: G 25 PHE cc_start: 0.8816 (m-10) cc_final: 0.7844 (m-10) REVERT: G 56 GLU cc_start: 0.8996 (tt0) cc_final: 0.7039 (tt0) REVERT: G 94 ASN cc_start: 0.9604 (t0) cc_final: 0.9266 (t0) REVERT: G 101 THR cc_start: 0.9138 (m) cc_final: 0.8659 (p) REVERT: H 59 MET cc_start: 0.9813 (mmp) cc_final: 0.9432 (mmm) REVERT: H 64 ASN cc_start: 0.9596 (m110) cc_final: 0.9280 (m110) REVERT: H 110 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8813 (mm-30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3154 time to fit residues: 74.2206 Evaluate side-chains 125 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.8044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15000 Z= 0.243 Angle : 0.652 11.220 21694 Z= 0.380 Chirality : 0.035 0.146 2468 Planarity : 0.004 0.047 1582 Dihedral : 31.982 176.805 4762 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 1.45 (0.28), residues: 882 helix: 1.31 (0.20), residues: 658 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 207 HIS 0.008 0.001 HIS H 106 PHE 0.020 0.002 PHE B 61 TYR 0.028 0.002 TYR H 37 ARG 0.007 0.000 ARG X 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9334 (mt-10) REVERT: A 62 ILE cc_start: 0.8951 (mm) cc_final: 0.8721 (mm) REVERT: A 81 ASP cc_start: 0.8823 (m-30) cc_final: 0.8494 (m-30) REVERT: A 90 MET cc_start: 0.9723 (mmp) cc_final: 0.9481 (mmm) REVERT: A 105 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 109 LEU cc_start: 0.9521 (mt) cc_final: 0.9073 (mt) REVERT: A 120 MET cc_start: 0.9342 (tpt) cc_final: 0.8934 (tpp) REVERT: A 126 LEU cc_start: 0.9611 (mm) cc_final: 0.9396 (tt) REVERT: B 63 GLU cc_start: 0.9567 (mt-10) cc_final: 0.8987 (tp30) REVERT: B 97 LEU cc_start: 0.9436 (tp) cc_final: 0.9147 (tp) REVERT: C 25 PHE cc_start: 0.8595 (m-10) cc_final: 0.8241 (m-10) REVERT: C 94 ASN cc_start: 0.9480 (t0) cc_final: 0.9116 (t0) REVERT: C 101 THR cc_start: 0.9368 (m) cc_final: 0.9036 (t) REVERT: D 34 TYR cc_start: 0.9537 (m-80) cc_final: 0.8874 (m-80) REVERT: D 59 MET cc_start: 0.9767 (mmm) cc_final: 0.9345 (mmm) REVERT: D 64 ASN cc_start: 0.9355 (m110) cc_final: 0.8951 (m110) REVERT: D 67 PHE cc_start: 0.9597 (t80) cc_final: 0.9291 (t80) REVERT: D 79 HIS cc_start: 0.9672 (t-90) cc_final: 0.9305 (t-90) REVERT: D 98 LEU cc_start: 0.9397 (mm) cc_final: 0.8926 (mm) REVERT: E 50 GLU cc_start: 0.9729 (mt-10) cc_final: 0.9492 (mt-10) REVERT: E 90 MET cc_start: 0.9598 (ttp) cc_final: 0.9295 (ttp) REVERT: E 99 TYR cc_start: 0.9483 (t80) cc_final: 0.9181 (t80) REVERT: G 25 PHE cc_start: 0.8784 (m-10) cc_final: 0.7885 (m-10) REVERT: G 56 GLU cc_start: 0.9002 (tt0) cc_final: 0.7198 (tt0) REVERT: G 94 ASN cc_start: 0.9575 (t0) cc_final: 0.9310 (t0) REVERT: G 101 THR cc_start: 0.9266 (m) cc_final: 0.8830 (p) REVERT: H 59 MET cc_start: 0.9774 (mmp) cc_final: 0.9483 (mmm) REVERT: H 64 ASN cc_start: 0.9529 (m110) cc_final: 0.9263 (m-40) REVERT: H 76 ARG cc_start: 0.9565 (ptp-110) cc_final: 0.9363 (ptt90) REVERT: H 110 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8799 (mm-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3159 time to fit residues: 73.0982 Evaluate side-chains 123 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038562 restraints weight = 184318.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038867 restraints weight = 119669.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039220 restraints weight = 84010.698| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.8582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15000 Z= 0.370 Angle : 0.722 13.470 21694 Z= 0.420 Chirality : 0.039 0.170 2468 Planarity : 0.005 0.045 1582 Dihedral : 32.517 177.545 4762 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 28.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 1.11 (0.27), residues: 882 helix: 1.06 (0.19), residues: 658 sheet: None (None), residues: 0 loop : 0.04 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP X 207 HIS 0.009 0.002 HIS F 75 PHE 0.021 0.002 PHE B 61 TYR 0.034 0.003 TYR H 37 ARG 0.006 0.001 ARG X 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.99 seconds wall clock time: 45 minutes 4.07 seconds (2704.07 seconds total)