Starting phenix.real_space_refine on Thu Sep 26 18:58:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/09_2024/8g8b_29845.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/09_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_29845/09_2024/8g8b_29845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/09_2024/8g8b_29845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/09_2024/8g8b_29845.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/09_2024/8g8b_29845.cif" } 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. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.03, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 969.5 milliseconds 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: 6.38 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: 5.99 Time building geometry restraints manager: 3.82 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: 0.00 - 2.36: 21469 2.36 - 4.72: 201 4.72 - 7.08: 20 7.08 - 9.44: 3 9.44 - 11.79: 1 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 3.120 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 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- 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 : 0.993 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: 0.3341 time to fit residues: 143.7303 Evaluate side-chains 187 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 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 64 ASN B 75 HIS B 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15000 Z= 0.345 Angle : 0.696 13.099 21694 Z= 0.409 Chirality : 0.038 0.207 2468 Planarity : 0.007 0.150 1582 Dihedral : 31.609 178.169 4762 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 1.74 (0.27), residues: 882 helix: 1.68 (0.19), residues: 665 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 207 HIS 0.009 0.002 HIS F 75 PHE 0.018 0.002 PHE X 278 TYR 0.028 0.003 TYR H 80 ARG 0.013 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 237 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.089 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: 0.9696 (mp) cc_final: 0.9452 (mt) REVERT: A 90 MET cc_start: 0.9716 (mmp) cc_final: 0.9452 (mmp) REVERT: A 92 LEU cc_start: 0.9830 (mt) cc_final: 0.9622 (mp) REVERT: A 106 ASP cc_start: 0.9459 (m-30) cc_final: 0.9219 (t0) REVERT: A 126 LEU cc_start: 0.9568 (mm) cc_final: 0.9295 (tp) REVERT: B 53 GLU cc_start: 0.9407 (tp30) cc_final: 0.9016 (tt0) REVERT: B 59 LYS cc_start: 0.9716 (tppp) cc_final: 0.9405 (tppt) REVERT: B 96 THR cc_start: 0.8887 (m) cc_final: 0.8471 (p) REVERT: B 97 LEU cc_start: 0.9452 (tp) cc_final: 0.8970 (tp) REVERT: C 25 PHE cc_start: 0.8448 (m-10) cc_final: 0.8207 (m-10) REVERT: C 94 ASN cc_start: 0.9649 (t0) cc_final: 0.9219 (t0) REVERT: C 101 THR cc_start: 0.9419 (m) cc_final: 0.9064 (t) REVERT: D 59 MET cc_start: 0.9850 (mmm) cc_final: 0.9411 (mmm) REVERT: D 64 ASN cc_start: 0.9589 (m-40) cc_final: 0.9209 (m-40) REVERT: D 79 HIS cc_start: 0.9744 (t-90) cc_final: 0.9540 (t-90) REVERT: E 74 ILE cc_start: 0.9725 (mt) cc_final: 0.9335 (mt) REVERT: E 94 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9103 (mm-30) REVERT: F 26 ILE cc_start: 0.9327 (tp) cc_final: 0.9093 (tp) REVERT: F 53 GLU cc_start: 0.9511 (tp30) cc_final: 0.9154 (tt0) REVERT: F 57 VAL cc_start: 0.9674 (t) cc_final: 0.9453 (p) REVERT: G 25 PHE cc_start: 0.9013 (m-80) cc_final: 0.8756 (m-10) REVERT: G 73 ASN cc_start: 0.9300 (m110) cc_final: 0.8953 (m110) REVERT: G 94 ASN cc_start: 0.9753 (t0) cc_final: 0.9319 (t0) REVERT: G 101 THR cc_start: 0.9339 (m) cc_final: 0.8925 (p) REVERT: H 34 TYR cc_start: 0.9537 (m-80) cc_final: 0.9170 (m-80) REVERT: H 64 ASN cc_start: 0.9644 (m-40) cc_final: 0.9414 (m110) REVERT: H 73 GLU cc_start: 0.9500 (tp30) cc_final: 0.8689 (tp30) REVERT: H 76 ARG cc_start: 0.9648 (mtm-85) cc_final: 0.9354 (ptp-110) REVERT: H 79 HIS cc_start: 0.9557 (t-90) cc_final: 0.9336 (t-90) REVERT: H 90 GLU cc_start: 0.9430 (mp0) cc_final: 0.9061 (mp0) REVERT: H 98 LEU cc_start: 0.9102 (mt) cc_final: 0.8849 (mt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3225 time to fit residues: 103.6889 Evaluate side-chains 165 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 38 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15000 Z= 0.362 Angle : 0.703 13.239 21694 Z= 0.410 Chirality : 0.038 0.144 2468 Planarity : 0.006 0.056 1582 Dihedral : 32.464 177.543 4762 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: 1.33 (0.27), residues: 882 helix: 1.31 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 207 HIS 0.010 0.002 HIS F 75 PHE 0.020 0.002 PHE F 61 TYR 0.032 0.003 TYR B 88 ARG 0.012 0.001 ARG D 96 *********************** 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 197 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.056 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: A 79 LYS cc_start: 0.9271 (mmtm) cc_final: 0.9005 (mmtm) REVERT: A 81 ASP cc_start: 0.9009 (m-30) cc_final: 0.8775 (m-30) REVERT: A 97 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8760 (mt-10) REVERT: A 103 LEU cc_start: 0.9508 (tt) cc_final: 0.9200 (tt) REVERT: A 126 LEU cc_start: 0.9604 (mm) cc_final: 0.9339 (tp) REVERT: B 53 GLU cc_start: 0.9508 (tp30) cc_final: 0.9271 (tt0) REVERT: B 96 THR cc_start: 0.9026 (m) cc_final: 0.8490 (m) REVERT: B 97 LEU cc_start: 0.9455 (tp) cc_final: 0.9081 (tp) REVERT: C 25 PHE cc_start: 0.8278 (m-10) cc_final: 0.8020 (m-10) REVERT: C 83 LEU cc_start: 0.9801 (mp) cc_final: 0.9382 (mp) REVERT: C 90 ASP cc_start: 0.8671 (t0) cc_final: 0.8411 (t70) REVERT: C 94 ASN cc_start: 0.9649 (t0) cc_final: 0.9197 (t0) REVERT: C 101 THR cc_start: 0.9419 (m) cc_final: 0.9004 (t) REVERT: D 58 ILE cc_start: 0.9849 (mt) cc_final: 0.9580 (mt) REVERT: D 59 MET cc_start: 0.9820 (mmm) cc_final: 0.9456 (mmm) REVERT: D 65 ASP cc_start: 0.9735 (t0) cc_final: 0.9358 (t0) REVERT: D 79 HIS cc_start: 0.9702 (t-90) cc_final: 0.9447 (t-90) REVERT: D 98 LEU cc_start: 0.9266 (mt) cc_final: 0.9052 (mm) REVERT: E 94 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9101 (mm-30) REVERT: E 99 TYR cc_start: 0.9376 (t80) cc_final: 0.8994 (t80) REVERT: F 53 GLU cc_start: 0.9648 (tp30) cc_final: 0.9326 (tt0) REVERT: F 57 VAL cc_start: 0.9685 (t) cc_final: 0.9343 (p) REVERT: F 58 LEU cc_start: 0.9780 (tp) cc_final: 0.9565 (mm) REVERT: F 59 LYS cc_start: 0.9699 (ptmm) cc_final: 0.9487 (ptmm) REVERT: F 74 GLU cc_start: 0.9234 (pp20) cc_final: 0.8740 (pp20) REVERT: F 100 PHE cc_start: 0.8613 (m-80) cc_final: 0.8287 (m-80) REVERT: G 25 PHE cc_start: 0.9011 (m-10) cc_final: 0.8679 (m-10) REVERT: G 73 ASN cc_start: 0.9273 (m110) cc_final: 0.8903 (m110) REVERT: G 79 ILE cc_start: 0.9754 (tp) cc_final: 0.9525 (pt) REVERT: G 94 ASN cc_start: 0.9667 (t0) cc_final: 0.9228 (t0) REVERT: G 101 THR cc_start: 0.9367 (m) cc_final: 0.8911 (p) REVERT: H 34 TYR cc_start: 0.9551 (m-80) cc_final: 0.8917 (m-80) REVERT: H 59 MET cc_start: 0.9840 (mmp) cc_final: 0.9549 (mmm) REVERT: H 69 ARG cc_start: 0.9070 (ptm160) cc_final: 0.8592 (ttt180) REVERT: H 73 GLU cc_start: 0.9535 (tp30) cc_final: 0.8858 (tp30) REVERT: H 79 HIS cc_start: 0.9548 (t-90) cc_final: 0.9328 (t-90) REVERT: H 117 LYS cc_start: 0.9705 (ptpp) cc_final: 0.9466 (ptmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3148 time to fit residues: 84.5949 Evaluate side-chains 149 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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: 20.0000 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 114 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS E 108 ASN H 92 GLN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15000 Z= 0.230 Angle : 0.626 11.894 21694 Z= 0.369 Chirality : 0.036 0.177 2468 Planarity : 0.005 0.069 1582 Dihedral : 32.077 176.663 4762 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 1.46 (0.27), residues: 882 helix: 1.40 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 207 HIS 0.006 0.001 HIS H 106 PHE 0.017 0.002 PHE A 67 TYR 0.019 0.002 TYR G 50 ARG 0.011 0.001 ARG A 131 *********************** 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 206 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.968 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 126 LEU cc_start: 0.9536 (mm) cc_final: 0.9259 (tp) REVERT: B 49 LEU cc_start: 0.9649 (mp) cc_final: 0.9183 (mp) REVERT: B 59 LYS cc_start: 0.9651 (tptm) cc_final: 0.9381 (tppt) REVERT: B 97 LEU cc_start: 0.9467 (tp) cc_final: 0.9097 (tp) REVERT: B 98 TYR cc_start: 0.8185 (m-10) cc_final: 0.7906 (m-10) REVERT: C 25 PHE cc_start: 0.8139 (m-10) cc_final: 0.7857 (m-10) REVERT: C 83 LEU cc_start: 0.9794 (mp) cc_final: 0.9424 (mp) REVERT: C 90 ASP cc_start: 0.8712 (t0) cc_final: 0.8459 (t70) REVERT: C 94 ASN cc_start: 0.9644 (t0) cc_final: 0.9208 (t0) REVERT: C 101 THR cc_start: 0.9451 (m) cc_final: 0.9123 (t) REVERT: C 112 GLN cc_start: 0.9517 (tp40) cc_final: 0.9040 (tp-100) REVERT: D 34 TYR cc_start: 0.9533 (m-80) cc_final: 0.9223 (m-80) REVERT: D 58 ILE cc_start: 0.9841 (mt) cc_final: 0.9557 (mt) REVERT: D 59 MET cc_start: 0.9796 (mmm) cc_final: 0.9444 (mmm) REVERT: D 65 ASP cc_start: 0.9635 (t0) cc_final: 0.9377 (t0) REVERT: D 79 HIS cc_start: 0.9714 (t-90) cc_final: 0.9472 (t-90) REVERT: D 103 LEU cc_start: 0.9604 (mt) cc_final: 0.9366 (mt) REVERT: E 94 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9024 (mm-30) REVERT: E 99 TYR cc_start: 0.9413 (t80) cc_final: 0.9048 (t80) REVERT: F 53 GLU cc_start: 0.9607 (tp30) cc_final: 0.9341 (tt0) REVERT: F 57 VAL cc_start: 0.9633 (t) cc_final: 0.9338 (p) REVERT: F 72 TYR cc_start: 0.9109 (m-80) cc_final: 0.8800 (m-80) REVERT: F 100 PHE cc_start: 0.8673 (m-80) cc_final: 0.8346 (m-80) REVERT: G 25 PHE cc_start: 0.9198 (m-10) cc_final: 0.8547 (m-10) REVERT: G 73 ASN cc_start: 0.9200 (m110) cc_final: 0.8843 (m110) REVERT: G 79 ILE cc_start: 0.9741 (tp) cc_final: 0.9534 (pt) REVERT: G 91 GLU cc_start: 0.9737 (pm20) cc_final: 0.9406 (pm20) REVERT: G 94 ASN cc_start: 0.9673 (t0) cc_final: 0.9301 (t0) REVERT: G 101 THR cc_start: 0.9357 (m) cc_final: 0.8886 (p) REVERT: H 34 TYR cc_start: 0.9514 (m-80) cc_final: 0.9076 (m-80) REVERT: H 59 MET cc_start: 0.9773 (mmp) cc_final: 0.9522 (mmm) REVERT: H 65 ASP cc_start: 0.9655 (t70) cc_final: 0.9372 (t0) REVERT: H 69 ARG cc_start: 0.9146 (ptm160) cc_final: 0.8939 (ptm160) REVERT: H 76 ARG cc_start: 0.9577 (ptp-110) cc_final: 0.9182 (mtm110) REVERT: H 79 HIS cc_start: 0.9534 (t-90) cc_final: 0.9301 (t-90) REVERT: H 90 GLU cc_start: 0.9548 (mp0) cc_final: 0.9261 (mp0) REVERT: H 110 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9073 (mm-30) REVERT: H 113 LYS cc_start: 0.9383 (ptpp) cc_final: 0.9055 (pttp) REVERT: H 117 LYS cc_start: 0.9702 (ptpp) cc_final: 0.9355 (ptmm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3159 time to fit residues: 88.8932 Evaluate side-chains 152 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15000 Z= 0.346 Angle : 0.691 14.864 21694 Z= 0.405 Chirality : 0.038 0.180 2468 Planarity : 0.006 0.055 1582 Dihedral : 32.521 177.084 4762 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 1.07 (0.27), residues: 882 helix: 1.12 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 207 HIS 0.006 0.002 HIS F 75 PHE 0.020 0.002 PHE B 61 TYR 0.018 0.002 TYR B 88 ARG 0.006 0.001 ARG X 282 *********************** 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 178 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.041 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: A 90 MET cc_start: 0.9711 (mmp) cc_final: 0.9509 (mmp) REVERT: A 126 LEU cc_start: 0.9638 (mm) cc_final: 0.9406 (tp) REVERT: B 59 LYS cc_start: 0.9677 (tptm) cc_final: 0.9442 (tppt) REVERT: B 66 ILE cc_start: 0.9648 (mt) cc_final: 0.9255 (tt) REVERT: B 97 LEU cc_start: 0.9455 (tp) cc_final: 0.9073 (tp) REVERT: B 98 TYR cc_start: 0.8264 (m-10) cc_final: 0.7865 (m-10) REVERT: C 25 PHE cc_start: 0.8084 (m-10) cc_final: 0.7747 (m-10) REVERT: C 83 LEU cc_start: 0.9801 (mp) cc_final: 0.9482 (mp) REVERT: C 90 ASP cc_start: 0.8772 (t0) cc_final: 0.8516 (t70) REVERT: C 94 ASN cc_start: 0.9674 (t0) cc_final: 0.9303 (t0) REVERT: C 101 THR cc_start: 0.9492 (m) cc_final: 0.9215 (p) REVERT: D 59 MET cc_start: 0.9826 (mmm) cc_final: 0.9570 (mmm) REVERT: D 79 HIS cc_start: 0.9727 (t-90) cc_final: 0.9320 (t-90) REVERT: D 98 LEU cc_start: 0.9395 (mm) cc_final: 0.9089 (mm) REVERT: E 85 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8537 (tp-100) REVERT: E 90 MET cc_start: 0.9604 (ttp) cc_final: 0.9359 (ptp) REVERT: E 94 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9032 (mm-30) REVERT: E 99 TYR cc_start: 0.9379 (t80) cc_final: 0.9019 (t80) REVERT: E 124 ILE cc_start: 0.9753 (mt) cc_final: 0.9327 (mt) REVERT: F 53 GLU cc_start: 0.9669 (tp30) cc_final: 0.9397 (tt0) REVERT: F 57 VAL cc_start: 0.9684 (t) cc_final: 0.9458 (p) REVERT: G 25 PHE cc_start: 0.9162 (m-10) cc_final: 0.8608 (m-10) REVERT: G 79 ILE cc_start: 0.9742 (tp) cc_final: 0.9542 (pt) REVERT: G 91 GLU cc_start: 0.9756 (pm20) cc_final: 0.9505 (pm20) REVERT: G 94 ASN cc_start: 0.9673 (t0) cc_final: 0.9278 (t0) REVERT: G 95 LYS cc_start: 0.9714 (ptpp) cc_final: 0.9460 (pttm) REVERT: G 101 THR cc_start: 0.9422 (m) cc_final: 0.9014 (p) REVERT: H 34 TYR cc_start: 0.9521 (m-80) cc_final: 0.9278 (m-80) REVERT: H 59 MET cc_start: 0.9819 (mmp) cc_final: 0.9534 (mmm) REVERT: H 64 ASN cc_start: 0.9663 (m-40) cc_final: 0.9362 (m-40) REVERT: H 70 ILE cc_start: 0.9936 (mm) cc_final: 0.9732 (mm) REVERT: H 73 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9220 (mt-10) REVERT: H 76 ARG cc_start: 0.9665 (ptp-110) cc_final: 0.9351 (mtm-85) REVERT: H 79 HIS cc_start: 0.9521 (t-90) cc_final: 0.9258 (t-90) REVERT: H 98 LEU cc_start: 0.9446 (tp) cc_final: 0.8771 (tp) REVERT: H 110 GLU cc_start: 0.9498 (mm-30) cc_final: 0.8941 (mm-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3249 time to fit residues: 78.7864 Evaluate side-chains 138 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15000 Z= 0.201 Angle : 0.620 11.437 21694 Z= 0.364 Chirality : 0.035 0.146 2468 Planarity : 0.004 0.049 1582 Dihedral : 32.000 176.104 4762 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 1.27 (0.27), residues: 882 helix: 1.24 (0.20), residues: 665 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.002 PHE A 67 TYR 0.032 0.002 TYR B 72 ARG 0.007 0.000 ARG D 89 *********************** 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 198 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.382 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: A 60 LEU cc_start: 0.9218 (mt) cc_final: 0.8416 (tp) REVERT: A 97 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8624 (mt-10) REVERT: A 126 LEU cc_start: 0.9631 (mm) cc_final: 0.9403 (tt) REVERT: B 59 LYS cc_start: 0.9622 (tptm) cc_final: 0.9354 (tppt) REVERT: B 97 LEU cc_start: 0.9385 (tp) cc_final: 0.8983 (tp) REVERT: B 98 TYR cc_start: 0.8201 (m-10) cc_final: 0.7924 (m-10) REVERT: C 25 PHE cc_start: 0.8444 (m-10) cc_final: 0.8232 (m-10) REVERT: C 83 LEU cc_start: 0.9807 (mp) cc_final: 0.9461 (mp) REVERT: C 90 ASP cc_start: 0.8772 (t0) cc_final: 0.8552 (t0) REVERT: C 94 ASN cc_start: 0.9677 (t0) cc_final: 0.9271 (t0) REVERT: C 101 THR cc_start: 0.9482 (m) cc_final: 0.9138 (t) REVERT: D 58 ILE cc_start: 0.9826 (mt) cc_final: 0.9615 (mt) REVERT: D 59 MET cc_start: 0.9798 (mmm) cc_final: 0.9548 (mmm) REVERT: D 64 ASN cc_start: 0.9404 (m-40) cc_final: 0.9018 (m-40) REVERT: D 65 ASP cc_start: 0.9606 (t70) cc_final: 0.9309 (t0) REVERT: D 79 HIS cc_start: 0.9733 (t-90) cc_final: 0.9347 (t-90) REVERT: D 103 LEU cc_start: 0.9632 (mt) cc_final: 0.9387 (mt) REVERT: E 90 MET cc_start: 0.9629 (ttp) cc_final: 0.9311 (ptp) REVERT: E 94 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8778 (mm-30) REVERT: E 99 TYR cc_start: 0.9494 (t80) cc_final: 0.9172 (t80) REVERT: E 124 ILE cc_start: 0.9756 (mt) cc_final: 0.9526 (mm) REVERT: F 53 GLU cc_start: 0.9591 (tp30) cc_final: 0.9340 (tt0) REVERT: F 72 TYR cc_start: 0.9122 (m-80) cc_final: 0.8698 (m-80) REVERT: G 25 PHE cc_start: 0.9022 (m-10) cc_final: 0.8501 (m-10) REVERT: G 73 ASN cc_start: 0.9127 (m110) cc_final: 0.8791 (m110) REVERT: G 94 ASN cc_start: 0.9722 (t0) cc_final: 0.9331 (m-40) REVERT: G 101 THR cc_start: 0.9452 (m) cc_final: 0.9049 (p) REVERT: H 34 TYR cc_start: 0.9501 (m-80) cc_final: 0.9150 (m-80) REVERT: H 59 MET cc_start: 0.9720 (mmp) cc_final: 0.9504 (mmm) REVERT: H 64 ASN cc_start: 0.9647 (m-40) cc_final: 0.9323 (m-40) REVERT: H 76 ARG cc_start: 0.9676 (ptp-110) cc_final: 0.9348 (mtm-85) REVERT: H 90 GLU cc_start: 0.9454 (mp0) cc_final: 0.9170 (mp0) REVERT: H 98 LEU cc_start: 0.9340 (tp) cc_final: 0.8676 (tp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3201 time to fit residues: 87.9423 Evaluate side-chains 152 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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: 9.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.7073 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= 0.252 Angle : 0.630 12.699 21694 Z= 0.369 Chirality : 0.035 0.152 2468 Planarity : 0.004 0.044 1582 Dihedral : 32.085 176.837 4762 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 1.23 (0.27), residues: 882 helix: 1.24 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.019 0.002 PHE B 61 TYR 0.045 0.002 TYR H 37 ARG 0.010 0.001 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 181 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.059 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 60 LEU cc_start: 0.9282 (mt) cc_final: 0.8592 (tp) REVERT: A 97 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8531 (mt-10) REVERT: A 126 LEU cc_start: 0.9637 (mm) cc_final: 0.9419 (tt) REVERT: B 66 ILE cc_start: 0.9600 (mt) cc_final: 0.9178 (tt) REVERT: B 97 LEU cc_start: 0.9432 (tp) cc_final: 0.9081 (tp) REVERT: B 98 TYR cc_start: 0.8264 (m-10) cc_final: 0.7882 (m-10) REVERT: C 25 PHE cc_start: 0.8241 (m-10) cc_final: 0.7890 (m-10) REVERT: C 83 LEU cc_start: 0.9799 (mp) cc_final: 0.9453 (mp) REVERT: C 90 ASP cc_start: 0.8809 (t0) cc_final: 0.8570 (t70) REVERT: C 94 ASN cc_start: 0.9669 (t0) cc_final: 0.9251 (t0) REVERT: C 101 THR cc_start: 0.9493 (m) cc_final: 0.9223 (p) REVERT: D 58 ILE cc_start: 0.9838 (mt) cc_final: 0.9636 (mt) REVERT: D 59 MET cc_start: 0.9813 (mmm) cc_final: 0.9568 (mmm) REVERT: D 64 ASN cc_start: 0.9390 (m-40) cc_final: 0.9028 (m-40) REVERT: D 65 ASP cc_start: 0.9629 (t70) cc_final: 0.9328 (t0) REVERT: D 79 HIS cc_start: 0.9709 (t-90) cc_final: 0.9312 (t-90) REVERT: D 103 LEU cc_start: 0.9601 (mt) cc_final: 0.9351 (mt) REVERT: E 68 GLN cc_start: 0.9457 (pp30) cc_final: 0.9188 (pp30) REVERT: E 90 MET cc_start: 0.9649 (ttp) cc_final: 0.9354 (ptp) REVERT: E 99 TYR cc_start: 0.9499 (t80) cc_final: 0.9162 (t80) REVERT: E 124 ILE cc_start: 0.9765 (mt) cc_final: 0.9280 (mt) REVERT: F 53 GLU cc_start: 0.9636 (tp30) cc_final: 0.9366 (tt0) REVERT: G 25 PHE cc_start: 0.8752 (m-10) cc_final: 0.7468 (m-10) REVERT: G 56 GLU cc_start: 0.8729 (tt0) cc_final: 0.6397 (tt0) REVERT: G 94 ASN cc_start: 0.9669 (t0) cc_final: 0.9232 (t0) REVERT: G 101 THR cc_start: 0.9397 (m) cc_final: 0.9000 (p) REVERT: H 59 MET cc_start: 0.9760 (mmp) cc_final: 0.9514 (mmm) REVERT: H 64 ASN cc_start: 0.9655 (m-40) cc_final: 0.9363 (m-40) REVERT: H 69 ARG cc_start: 0.9355 (ptm160) cc_final: 0.9125 (ptp-170) REVERT: H 70 ILE cc_start: 0.9924 (mm) cc_final: 0.9676 (mm) REVERT: H 76 ARG cc_start: 0.9709 (ptp-110) cc_final: 0.9313 (mtm-85) REVERT: H 90 GLU cc_start: 0.9337 (mp0) cc_final: 0.9059 (mp0) REVERT: H 98 LEU cc_start: 0.9012 (tp) cc_final: 0.8586 (tp) REVERT: H 103 LEU cc_start: 0.9684 (mt) cc_final: 0.9407 (mt) REVERT: H 113 LYS cc_start: 0.9607 (pttm) cc_final: 0.9259 (ptpp) REVERT: H 117 LYS cc_start: 0.9698 (ptpp) cc_final: 0.9447 (ptmm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3045 time to fit residues: 75.9968 Evaluate side-chains 134 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15000 Z= 0.186 Angle : 0.610 10.987 21694 Z= 0.358 Chirality : 0.035 0.182 2468 Planarity : 0.004 0.049 1582 Dihedral : 31.750 176.248 4762 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 1.41 (0.28), residues: 882 helix: 1.35 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.11 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.002 0.001 HIS F 75 PHE 0.018 0.001 PHE B 61 TYR 0.032 0.002 TYR H 37 ARG 0.003 0.000 ARG H 96 *********************** 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 197 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.986 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: A 60 LEU cc_start: 0.9225 (mt) cc_final: 0.8445 (tp) REVERT: A 81 ASP cc_start: 0.8798 (m-30) cc_final: 0.8570 (m-30) REVERT: A 82 LEU cc_start: 0.9027 (mt) cc_final: 0.8776 (mt) REVERT: A 97 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8722 (mt-10) REVERT: A 105 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 109 LEU cc_start: 0.9499 (mt) cc_final: 0.9107 (mt) REVERT: A 126 LEU cc_start: 0.9604 (mm) cc_final: 0.9388 (tt) REVERT: B 59 LYS cc_start: 0.9393 (tptp) cc_final: 0.9155 (tppt) REVERT: B 63 GLU cc_start: 0.9640 (mt-10) cc_final: 0.9014 (mt-10) REVERT: B 97 LEU cc_start: 0.9402 (tp) cc_final: 0.9045 (tp) REVERT: B 98 TYR cc_start: 0.8151 (m-10) cc_final: 0.7861 (m-10) REVERT: C 25 PHE cc_start: 0.8440 (m-10) cc_final: 0.8169 (m-10) REVERT: C 83 LEU cc_start: 0.9798 (mp) cc_final: 0.9450 (mp) REVERT: C 90 ASP cc_start: 0.8679 (t0) cc_final: 0.8445 (t0) REVERT: C 94 ASN cc_start: 0.9664 (t0) cc_final: 0.9245 (t0) REVERT: C 101 THR cc_start: 0.9489 (m) cc_final: 0.9208 (p) REVERT: D 58 ILE cc_start: 0.9825 (mt) cc_final: 0.9606 (mt) REVERT: D 59 MET cc_start: 0.9797 (mmm) cc_final: 0.9524 (mmm) REVERT: D 64 ASN cc_start: 0.9422 (m-40) cc_final: 0.9035 (m-40) REVERT: D 65 ASP cc_start: 0.9620 (t70) cc_final: 0.9317 (t0) REVERT: D 79 HIS cc_start: 0.9731 (t-90) cc_final: 0.9479 (t-90) REVERT: D 103 LEU cc_start: 0.9557 (mt) cc_final: 0.9333 (mt) REVERT: E 90 MET cc_start: 0.9558 (ttp) cc_final: 0.9298 (ptp) REVERT: E 124 ILE cc_start: 0.9790 (mt) cc_final: 0.9455 (mt) REVERT: F 53 GLU cc_start: 0.9629 (tp30) cc_final: 0.9363 (tt0) REVERT: F 72 TYR cc_start: 0.9150 (m-80) cc_final: 0.8712 (m-80) REVERT: G 25 PHE cc_start: 0.8785 (m-10) cc_final: 0.7617 (m-10) REVERT: G 41 GLU cc_start: 0.9227 (pm20) cc_final: 0.8986 (pm20) REVERT: G 56 GLU cc_start: 0.8792 (tt0) cc_final: 0.6902 (tt0) REVERT: G 94 ASN cc_start: 0.9717 (t0) cc_final: 0.9352 (m-40) REVERT: G 101 THR cc_start: 0.9389 (m) cc_final: 0.9006 (p) REVERT: H 59 MET cc_start: 0.9753 (mmp) cc_final: 0.9540 (mmm) REVERT: H 64 ASN cc_start: 0.9601 (m-40) cc_final: 0.9348 (m110) REVERT: H 70 ILE cc_start: 0.9901 (mm) cc_final: 0.9644 (mm) REVERT: H 76 ARG cc_start: 0.9725 (ptp-110) cc_final: 0.9358 (mtm-85) REVERT: H 97 LEU cc_start: 0.9674 (tt) cc_final: 0.9471 (tt) REVERT: H 98 LEU cc_start: 0.8966 (tp) cc_final: 0.8682 (tp) REVERT: H 103 LEU cc_start: 0.9672 (mt) cc_final: 0.9414 (mt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3037 time to fit residues: 82.7512 Evaluate side-chains 149 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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: 20.0000 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15000 Z= 0.251 Angle : 0.642 14.192 21694 Z= 0.376 Chirality : 0.036 0.208 2468 Planarity : 0.004 0.048 1582 Dihedral : 31.915 177.191 4762 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.29 (0.28), residues: 882 helix: 1.25 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP X 207 HIS 0.004 0.001 HIS F 75 PHE 0.030 0.002 PHE X 249 TYR 0.048 0.003 TYR F 88 ARG 0.005 0.000 ARG X 282 *********************** 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 182 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.066 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 60 LEU cc_start: 0.9293 (mt) cc_final: 0.8589 (tp) REVERT: A 81 ASP cc_start: 0.8866 (m-30) cc_final: 0.8551 (m-30) REVERT: A 90 MET cc_start: 0.9719 (mmp) cc_final: 0.9506 (mmp) REVERT: A 97 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8399 (mt-10) REVERT: A 105 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 106 ASP cc_start: 0.9329 (p0) cc_final: 0.8962 (p0) REVERT: A 109 LEU cc_start: 0.9498 (mt) cc_final: 0.9110 (mt) REVERT: A 110 CYS cc_start: 0.9774 (m) cc_final: 0.9425 (t) REVERT: A 126 LEU cc_start: 0.9618 (mm) cc_final: 0.9367 (tt) REVERT: B 59 LYS cc_start: 0.9402 (tptp) cc_final: 0.9110 (tppt) REVERT: B 66 ILE cc_start: 0.9631 (mt) cc_final: 0.9215 (tt) REVERT: B 97 LEU cc_start: 0.9396 (tp) cc_final: 0.9163 (tp) REVERT: B 98 TYR cc_start: 0.8310 (m-10) cc_final: 0.8088 (m-10) REVERT: C 25 PHE cc_start: 0.8233 (m-10) cc_final: 0.7869 (m-10) REVERT: C 83 LEU cc_start: 0.9795 (mp) cc_final: 0.9439 (mp) REVERT: C 90 ASP cc_start: 0.8797 (t0) cc_final: 0.8559 (t70) REVERT: C 94 ASN cc_start: 0.9667 (t0) cc_final: 0.9247 (t0) REVERT: C 101 THR cc_start: 0.9497 (m) cc_final: 0.9219 (p) REVERT: D 58 ILE cc_start: 0.9839 (mt) cc_final: 0.9632 (mt) REVERT: D 59 MET cc_start: 0.9811 (mmm) cc_final: 0.9549 (mmm) REVERT: D 64 ASN cc_start: 0.9450 (m-40) cc_final: 0.9073 (m-40) REVERT: D 65 ASP cc_start: 0.9442 (t70) cc_final: 0.9032 (t0) REVERT: D 79 HIS cc_start: 0.9712 (t-90) cc_final: 0.9043 (t-90) REVERT: D 98 LEU cc_start: 0.9226 (mm) cc_final: 0.8946 (mm) REVERT: D 103 LEU cc_start: 0.9518 (mt) cc_final: 0.9256 (mt) REVERT: E 68 GLN cc_start: 0.9439 (pp30) cc_final: 0.9166 (pp30) REVERT: E 90 MET cc_start: 0.9576 (ttp) cc_final: 0.9184 (ptp) REVERT: E 99 TYR cc_start: 0.9451 (t80) cc_final: 0.9145 (t80) REVERT: E 124 ILE cc_start: 0.9775 (mt) cc_final: 0.9323 (mt) REVERT: F 53 GLU cc_start: 0.9684 (tp30) cc_final: 0.9386 (tt0) REVERT: F 60 VAL cc_start: 0.9764 (t) cc_final: 0.9388 (t) REVERT: G 25 PHE cc_start: 0.8866 (m-10) cc_final: 0.7848 (m-10) REVERT: G 41 GLU cc_start: 0.9175 (pm20) cc_final: 0.8925 (pm20) REVERT: G 56 GLU cc_start: 0.8886 (tt0) cc_final: 0.7115 (tt0) REVERT: G 94 ASN cc_start: 0.9694 (t0) cc_final: 0.9335 (t0) REVERT: G 101 THR cc_start: 0.9432 (m) cc_final: 0.9020 (p) REVERT: H 59 MET cc_start: 0.9749 (mmp) cc_final: 0.9520 (mmm) REVERT: H 64 ASN cc_start: 0.9603 (m-40) cc_final: 0.9308 (m110) REVERT: H 76 ARG cc_start: 0.9694 (ptp-110) cc_final: 0.9493 (mtm110) REVERT: H 79 HIS cc_start: 0.9684 (t-90) cc_final: 0.9407 (t-90) REVERT: H 113 LYS cc_start: 0.9635 (pttm) cc_final: 0.9214 (ptpp) REVERT: H 117 LYS cc_start: 0.9684 (ptpp) cc_final: 0.9429 (ptmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3095 time to fit residues: 77.4997 Evaluate side-chains 136 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 0.0270 chunk 77 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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: 0.8055 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15000 Z= 0.189 Angle : 0.641 11.611 21694 Z= 0.372 Chirality : 0.036 0.185 2468 Planarity : 0.004 0.052 1582 Dihedral : 31.624 176.201 4762 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 882 helix: 1.20 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP X 207 HIS 0.006 0.001 HIS F 75 PHE 0.022 0.002 PHE B 61 TYR 0.039 0.002 TYR H 80 ARG 0.005 0.000 ARG D 76 ********************** 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 193 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.130 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: A 60 LEU cc_start: 0.9227 (mt) cc_final: 0.8597 (tp) REVERT: A 80 THR cc_start: 0.8624 (t) cc_final: 0.8325 (p) REVERT: A 81 ASP cc_start: 0.8827 (m-30) cc_final: 0.8467 (m-30) REVERT: A 97 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8654 (mt-10) REVERT: A 105 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 106 ASP cc_start: 0.9291 (p0) cc_final: 0.8925 (p0) REVERT: A 109 LEU cc_start: 0.9508 (mt) cc_final: 0.9085 (mt) REVERT: A 110 CYS cc_start: 0.9710 (m) cc_final: 0.9392 (t) REVERT: A 126 LEU cc_start: 0.9623 (mm) cc_final: 0.9388 (tt) REVERT: B 46 ILE cc_start: 0.9567 (mm) cc_final: 0.9302 (tp) REVERT: B 59 LYS cc_start: 0.9317 (tptp) cc_final: 0.9056 (tppt) REVERT: B 63 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9023 (mt-10) REVERT: B 97 LEU cc_start: 0.9392 (tp) cc_final: 0.9133 (tp) REVERT: B 98 TYR cc_start: 0.8269 (m-10) cc_final: 0.8000 (m-10) REVERT: C 25 PHE cc_start: 0.8456 (m-10) cc_final: 0.8245 (m-10) REVERT: C 83 LEU cc_start: 0.9800 (mp) cc_final: 0.9442 (mp) REVERT: C 90 ASP cc_start: 0.8730 (t0) cc_final: 0.8485 (t0) REVERT: C 94 ASN cc_start: 0.9665 (t0) cc_final: 0.9257 (t0) REVERT: C 101 THR cc_start: 0.9486 (m) cc_final: 0.9202 (p) REVERT: D 58 ILE cc_start: 0.9827 (mt) cc_final: 0.9601 (mt) REVERT: D 59 MET cc_start: 0.9803 (mmm) cc_final: 0.9530 (mmm) REVERT: D 64 ASN cc_start: 0.9445 (m-40) cc_final: 0.8972 (m-40) REVERT: D 65 ASP cc_start: 0.9431 (t70) cc_final: 0.9189 (t0) REVERT: D 79 HIS cc_start: 0.9615 (t-90) cc_final: 0.9107 (t-90) REVERT: D 98 LEU cc_start: 0.9010 (mm) cc_final: 0.8132 (mm) REVERT: D 103 LEU cc_start: 0.9495 (mt) cc_final: 0.9225 (mt) REVERT: E 81 ASP cc_start: 0.9130 (m-30) cc_final: 0.8815 (m-30) REVERT: E 90 MET cc_start: 0.9564 (ttp) cc_final: 0.9299 (ptp) REVERT: E 124 ILE cc_start: 0.9778 (mt) cc_final: 0.9454 (mt) REVERT: F 53 GLU cc_start: 0.9635 (tp30) cc_final: 0.9383 (tt0) REVERT: F 72 TYR cc_start: 0.9036 (m-80) cc_final: 0.8740 (m-10) REVERT: G 25 PHE cc_start: 0.8879 (m-10) cc_final: 0.8018 (m-10) REVERT: G 56 GLU cc_start: 0.8903 (tt0) cc_final: 0.7109 (tt0) REVERT: G 94 ASN cc_start: 0.9661 (t0) cc_final: 0.9332 (m-40) REVERT: G 101 THR cc_start: 0.9375 (m) cc_final: 0.8974 (p) REVERT: H 59 MET cc_start: 0.9663 (mmp) cc_final: 0.9452 (mmm) REVERT: H 64 ASN cc_start: 0.9583 (m-40) cc_final: 0.9263 (m-40) REVERT: H 76 ARG cc_start: 0.9681 (ptp-110) cc_final: 0.9476 (mtm110) REVERT: H 79 HIS cc_start: 0.9669 (t-90) cc_final: 0.9433 (t-90) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2997 time to fit residues: 80.3566 Evaluate side-chains 144 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.052338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039797 restraints weight = 181660.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.040334 restraints weight = 107875.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040840 restraints weight = 75001.562| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15000 Z= 0.351 Angle : 0.717 14.712 21694 Z= 0.416 Chirality : 0.039 0.211 2468 Planarity : 0.006 0.049 1582 Dihedral : 32.262 177.877 4762 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 0.90 (0.27), residues: 882 helix: 0.97 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP X 207 HIS 0.005 0.001 HIS A 113 PHE 0.021 0.003 PHE G 25 TYR 0.034 0.003 TYR H 80 ARG 0.008 0.001 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.59 seconds wall clock time: 44 minutes 54.02 seconds (2694.02 seconds total)