Starting phenix.real_space_refine on Wed Sep 25 22:27:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/09_2024/7wlr_32591.cif" } resolution = 3.54 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= 1.000 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 289 5.49 5 S 6 5.16 5 C 6588 2.51 5 N 2222 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 11922 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 666 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 714 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.89, per 1000 atoms: 0.58 Number of scatterers: 11922 At special positions: 0 Unit cell: (118.72, 86.92, 119.78, 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 6 16.00 P 289 15.00 O 2817 8.00 N 2222 7.00 C 6588 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: 2.73 Conformation dependent library (CDL) restraints added in 947.4 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.5% alpha, 3.2% beta 144 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 4.142A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.688A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.755A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.815A 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: 4.439A pdb=" N VAL C 49 " --> pdb=" O SER 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 'D' and resid 41 through 53 removed outlier: 3.925A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 removed outlier: 3.510A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 107 through 129 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.880A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.642A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.507A pdb=" N ILE E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.999A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.426A pdb=" N VAL G 49 " --> pdb=" O SER 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 41 through 53 Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 107 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.306A pdb=" N ARG A 84 " --> 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 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.520A 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: 7.377A pdb=" N ARG C 42 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG E 84 " --> 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 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 93 " (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 78 418 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1476 1.32 - 1.44: 4699 1.44 - 1.56: 5959 1.56 - 1.69: 577 1.69 - 1.81: 10 Bond restraints: 12721 Sorted by residual: bond pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.29e-02 6.01e+03 1.75e+01 bond pdb=" C ARG B 35 " pdb=" O ARG B 35 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" CZ ARG C 32 " pdb=" NH2 ARG C 32 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 bond pdb=" CZ ARG F 35 " pdb=" NH2 ARG F 35 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 135 " pdb=" NH2 ARG A 135 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 16892 1.55 - 3.10: 1297 3.10 - 4.65: 178 4.65 - 6.20: 44 6.20 - 7.74: 13 Bond angle restraints: 18424 Sorted by residual: angle pdb=" C THR A 59 " pdb=" N GLU A 60 " pdb=" CA GLU A 60 " ideal model delta sigma weight residual 120.82 127.74 -6.92 1.47e+00 4.63e-01 2.22e+01 angle pdb=" C SER G 14 " pdb=" N THR G 15 " pdb=" CA THR G 15 " ideal model delta sigma weight residual 120.90 127.52 -6.62 1.41e+00 5.03e-01 2.21e+01 angle pdb=" N ARG F 23 " pdb=" CA ARG F 23 " pdb=" C ARG F 23 " ideal model delta sigma weight residual 111.34 118.15 -6.81 1.49e+00 4.50e-01 2.09e+01 angle pdb=" N GLU G 91 " pdb=" CA GLU G 91 " pdb=" C GLU G 91 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.84e+01 angle pdb=" O GLY D 108 " pdb=" C GLY D 108 " pdb=" N GLU D 109 " ideal model delta sigma weight residual 122.13 118.01 4.12 9.90e-01 1.02e+00 1.74e+01 ... (remaining 18419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 4488 21.23 - 42.46: 1286 42.46 - 63.69: 1085 63.69 - 84.92: 46 84.92 - 106.15: 8 Dihedral angle restraints: 6913 sinusoidal: 4719 harmonic: 2194 Sorted by residual: dihedral pdb=" CA GLY E 45 " pdb=" C GLY E 45 " pdb=" N THR E 46 " pdb=" CA THR E 46 " ideal model delta harmonic sigma weight residual 180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY A 45 " pdb=" C GLY A 45 " pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta harmonic sigma weight residual 180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1787 0.062 - 0.124: 281 0.124 - 0.187: 25 0.187 - 0.249: 10 0.249 - 0.311: 4 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA ARG F 23 " pdb=" N ARG F 23 " pdb=" C ARG F 23 " pdb=" CB ARG F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LYS G 118 " pdb=" N LYS G 118 " pdb=" C LYS G 118 " pdb=" CB LYS G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2104 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " 0.045 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR D 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 101 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY B 101 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY B 101 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 53 " 0.014 2.00e-02 2.50e+03 3.24e-02 1.57e+01 pdb=" CG HIS H 53 " -0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS H 53 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS H 53 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS H 53 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS H 53 " 0.055 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1741 2.77 - 3.30: 10480 3.30 - 3.83: 23372 3.83 - 4.37: 27505 4.37 - 4.90: 39362 Nonbonded interactions: 102460 Sorted by model distance: nonbonded pdb=" O2 DC I 50 " pdb=" N2 DG J 96 " model vdw 2.232 2.496 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 72 " model vdw 2.287 3.040 nonbonded pdb=" OG SER H 94 " pdb=" OE1 GLU H 97 " model vdw 2.346 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.365 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.383 3.040 ... (remaining 102455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 38 through 129) 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=1.00 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.460 Find NCS groups from input model: 0.280 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.006 0.060 12721 Z= 0.363 Angle : 0.884 7.744 18424 Z= 0.569 Chirality : 0.049 0.311 2107 Planarity : 0.010 0.124 1323 Dihedral : 29.271 106.152 5493 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 (0.29), residues: 738 helix: 1.78 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.047 0.003 HIS H 53 PHE 0.008 0.001 PHE D 74 TYR 0.068 0.004 TYR D 44 ARG 0.012 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.898 Fit side-chains REVERT: B 91 LYS cc_start: 0.7799 (tttp) cc_final: 0.7208 (ttmm) REVERT: C 41 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7399 (mt0) REVERT: C 95 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7248 (tttm) REVERT: D 38 LYS cc_start: 0.7201 (tptm) cc_final: 0.6779 (tppt) REVERT: D 89 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7467 (mttm) REVERT: E 111 CYS cc_start: 0.6645 (p) cc_final: 0.6433 (p) REVERT: G 36 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6569 (mmt90) REVERT: G 107 VAL cc_start: 0.8850 (p) cc_final: 0.8620 (m) REVERT: H 75 GLU cc_start: 0.6979 (tp30) cc_final: 0.6624 (mt-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3959 time to fit residues: 53.9766 Evaluate side-chains 62 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 53 HIS D 88 ASN E 77 GLN E 94 GLN F 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12721 Z= 0.200 Angle : 0.561 6.645 18424 Z= 0.342 Chirality : 0.034 0.129 2107 Planarity : 0.004 0.042 1323 Dihedral : 31.191 93.920 4005 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.47 % Allowed : 5.96 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.30), residues: 738 helix: 2.57 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.54 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE H 74 TYR 0.012 0.001 TYR G 57 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.877 Fit side-chains REVERT: A 77 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 91 LYS cc_start: 0.7868 (tttp) cc_final: 0.7326 (ttmm) REVERT: C 41 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7522 (mt0) REVERT: C 95 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7244 (tttm) REVERT: D 46 TYR cc_start: 0.7746 (t80) cc_final: 0.6976 (t80) REVERT: D 66 MET cc_start: 0.8726 (mmm) cc_final: 0.8405 (mmm) REVERT: D 89 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7470 (mttm) REVERT: E 77 GLN cc_start: 0.7852 (tt0) cc_final: 0.7577 (tt0) REVERT: G 36 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6674 (mmt90) REVERT: H 39 GLU cc_start: 0.7261 (pt0) cc_final: 0.6727 (mm-30) REVERT: H 88 ASN cc_start: 0.8020 (m110) cc_final: 0.7818 (m110) outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.2962 time to fit residues: 32.1346 Evaluate side-chains 65 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 51 GLN D 53 HIS F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12721 Z= 0.178 Angle : 0.539 6.774 18424 Z= 0.331 Chirality : 0.033 0.153 2107 Planarity : 0.004 0.035 1323 Dihedral : 31.152 94.311 4005 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.47 % Allowed : 9.25 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.30), residues: 738 helix: 2.78 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.005 0.001 PHE H 74 TYR 0.012 0.001 TYR G 57 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.922 Fit side-chains REVERT: A 77 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 91 LYS cc_start: 0.7891 (tttp) cc_final: 0.7326 (ttmm) REVERT: C 41 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7585 (mt0) REVERT: C 95 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7275 (tttm) REVERT: D 46 TYR cc_start: 0.7757 (t80) cc_final: 0.6927 (t80) REVERT: D 66 MET cc_start: 0.8752 (mmm) cc_final: 0.8508 (mmm) REVERT: D 89 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7422 (mttm) REVERT: E 77 GLN cc_start: 0.7848 (tt0) cc_final: 0.7588 (tt0) REVERT: G 36 ARG cc_start: 0.7095 (tpp80) cc_final: 0.6674 (mmt90) REVERT: H 39 GLU cc_start: 0.7360 (pt0) cc_final: 0.6814 (mm-30) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.2926 time to fit residues: 28.7457 Evaluate side-chains 66 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12721 Z= 0.275 Angle : 0.581 7.996 18424 Z= 0.349 Chirality : 0.036 0.141 2107 Planarity : 0.004 0.035 1323 Dihedral : 31.111 99.482 4005 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.94 % Allowed : 9.40 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 738 helix: 2.54 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE H 69 TYR 0.012 0.002 TYR B 51 ARG 0.003 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.783 Fit side-chains REVERT: A 77 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 91 LYS cc_start: 0.8009 (tttp) cc_final: 0.7472 (ttmm) REVERT: C 41 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7756 (mt0) REVERT: C 95 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7405 (tttm) REVERT: D 38 LYS cc_start: 0.7456 (tptm) cc_final: 0.7117 (tppt) REVERT: D 46 TYR cc_start: 0.7732 (t80) cc_final: 0.7023 (t80) REVERT: D 89 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7436 (mttm) REVERT: G 36 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6665 (mmt90) REVERT: G 61 GLU cc_start: 0.7068 (tp30) cc_final: 0.6784 (tt0) REVERT: G 76 SER cc_start: 0.8173 (p) cc_final: 0.7877 (p) REVERT: H 38 LYS cc_start: 0.7094 (tppt) cc_final: 0.6295 (mtpt) REVERT: H 39 GLU cc_start: 0.7739 (pt0) cc_final: 0.7397 (mm-30) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.3124 time to fit residues: 32.8289 Evaluate side-chains 70 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 94 GLN H 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12721 Z= 0.165 Angle : 0.517 6.970 18424 Z= 0.319 Chirality : 0.032 0.136 2107 Planarity : 0.003 0.036 1323 Dihedral : 30.637 95.669 4005 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.94 % Allowed : 10.03 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.30), residues: 738 helix: 2.91 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.64 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 68 TYR 0.010 0.001 TYR G 57 ARG 0.003 0.000 ARG H 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.939 Fit side-chains REVERT: A 77 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 91 LYS cc_start: 0.7955 (tttp) cc_final: 0.7412 (ttmm) REVERT: C 41 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7734 (mt0) REVERT: C 95 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7423 (tttm) REVERT: D 46 TYR cc_start: 0.7717 (t80) cc_final: 0.6833 (t80) REVERT: D 63 MET cc_start: 0.8702 (tpp) cc_final: 0.8390 (mmm) REVERT: D 89 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7433 (mttm) REVERT: E 62 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7985 (mm) REVERT: G 36 ARG cc_start: 0.7278 (tpp80) cc_final: 0.6783 (mmt90) REVERT: G 76 SER cc_start: 0.8124 (p) cc_final: 0.7818 (p) REVERT: H 38 LYS cc_start: 0.7218 (tppt) cc_final: 0.6363 (mtpt) REVERT: H 39 GLU cc_start: 0.7727 (pt0) cc_final: 0.7424 (mm-30) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.2896 time to fit residues: 31.6764 Evaluate side-chains 76 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.0010 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12721 Z= 0.194 Angle : 0.526 6.559 18424 Z= 0.322 Chirality : 0.033 0.137 2107 Planarity : 0.004 0.035 1323 Dihedral : 30.704 96.267 4005 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.41 % Allowed : 10.03 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.30), residues: 738 helix: 2.96 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.68 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE A 68 TYR 0.009 0.001 TYR G 57 ARG 0.003 0.000 ARG H 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.839 Fit side-chains REVERT: A 77 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 91 LYS cc_start: 0.7989 (tttp) cc_final: 0.7429 (ttmm) REVERT: C 41 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7743 (mt0) REVERT: C 95 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7409 (tttm) REVERT: D 38 LYS cc_start: 0.7619 (tptm) cc_final: 0.7241 (tppt) REVERT: D 46 TYR cc_start: 0.7768 (t80) cc_final: 0.6891 (t80) REVERT: D 89 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7406 (mttm) REVERT: E 62 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8022 (mm) REVERT: G 36 ARG cc_start: 0.7422 (tpp80) cc_final: 0.6896 (mmt90) REVERT: G 76 SER cc_start: 0.8164 (p) cc_final: 0.7852 (p) REVERT: H 38 LYS cc_start: 0.7295 (tppt) cc_final: 0.6417 (mtpt) REVERT: H 39 GLU cc_start: 0.7740 (pt0) cc_final: 0.7448 (mm-30) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.2686 time to fit residues: 28.1333 Evaluate side-chains 76 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12721 Z= 0.164 Angle : 0.508 6.013 18424 Z= 0.313 Chirality : 0.032 0.132 2107 Planarity : 0.003 0.036 1323 Dihedral : 30.534 94.750 4005 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.57 % Allowed : 10.03 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.30), residues: 738 helix: 3.12 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE D 74 TYR 0.008 0.001 TYR G 57 ARG 0.002 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.918 Fit side-chains REVERT: A 77 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 91 LYS cc_start: 0.7967 (tttp) cc_final: 0.7377 (ttmm) REVERT: C 41 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7733 (mt0) REVERT: C 95 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7414 (tttm) REVERT: D 38 LYS cc_start: 0.7698 (tptm) cc_final: 0.7323 (tppt) REVERT: D 46 TYR cc_start: 0.7733 (t80) cc_final: 0.6851 (t80) REVERT: D 89 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7435 (mttm) REVERT: E 62 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7969 (mm) REVERT: E 66 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7560 (mp) REVERT: G 36 ARG cc_start: 0.7325 (tpp80) cc_final: 0.6806 (mmt90) REVERT: G 76 SER cc_start: 0.8116 (p) cc_final: 0.7813 (p) REVERT: H 38 LYS cc_start: 0.7356 (tppt) cc_final: 0.6448 (mtpt) REVERT: H 39 GLU cc_start: 0.7782 (pt0) cc_final: 0.7479 (mm-30) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.2756 time to fit residues: 27.9873 Evaluate side-chains 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN H 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12721 Z= 0.373 Angle : 0.615 8.701 18424 Z= 0.362 Chirality : 0.037 0.146 2107 Planarity : 0.004 0.037 1323 Dihedral : 31.061 100.481 4005 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.04 % Allowed : 9.56 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.30), residues: 738 helix: 2.59 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.06 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 53 PHE 0.009 0.002 PHE H 69 TYR 0.014 0.002 TYR B 51 ARG 0.004 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.774 Fit side-chains REVERT: A 77 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 91 LYS cc_start: 0.8139 (tttp) cc_final: 0.7517 (ttmm) REVERT: C 41 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7909 (mt0) REVERT: C 95 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7406 (tttm) REVERT: D 38 LYS cc_start: 0.7808 (tptm) cc_final: 0.7472 (tppt) REVERT: D 46 TYR cc_start: 0.7854 (t80) cc_final: 0.7109 (t80) REVERT: D 89 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7427 (mttm) REVERT: E 66 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7718 (mm) REVERT: G 36 ARG cc_start: 0.7400 (tpp80) cc_final: 0.6881 (mmt90) REVERT: G 76 SER cc_start: 0.8047 (p) cc_final: 0.7764 (p) REVERT: H 39 GLU cc_start: 0.7843 (pt0) cc_final: 0.7548 (mm-30) REVERT: H 75 GLU cc_start: 0.7318 (tp30) cc_final: 0.6756 (mt-10) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.2775 time to fit residues: 29.2875 Evaluate side-chains 71 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12721 Z= 0.173 Angle : 0.520 8.578 18424 Z= 0.318 Chirality : 0.032 0.137 2107 Planarity : 0.004 0.036 1323 Dihedral : 30.604 97.163 4005 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.10 % Allowed : 10.66 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.30), residues: 738 helix: 2.98 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 68 TYR 0.010 0.001 TYR G 57 ARG 0.002 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.852 Fit side-chains REVERT: A 77 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 91 LYS cc_start: 0.7993 (tttp) cc_final: 0.7437 (ttmm) REVERT: C 41 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7777 (mt0) REVERT: C 95 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7398 (tttm) REVERT: D 38 LYS cc_start: 0.7703 (tptm) cc_final: 0.7465 (tppt) REVERT: D 46 TYR cc_start: 0.7742 (t80) cc_final: 0.6846 (t80) REVERT: D 89 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7413 (mttm) REVERT: E 66 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7574 (mp) REVERT: G 36 ARG cc_start: 0.7416 (tpp80) cc_final: 0.6922 (mmt90) REVERT: G 76 SER cc_start: 0.8011 (p) cc_final: 0.7712 (p) REVERT: H 39 GLU cc_start: 0.7824 (pt0) cc_final: 0.7546 (mm-30) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.2715 time to fit residues: 29.7527 Evaluate side-chains 76 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12721 Z= 0.225 Angle : 0.533 7.613 18424 Z= 0.324 Chirality : 0.033 0.140 2107 Planarity : 0.004 0.034 1323 Dihedral : 30.719 98.336 4005 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 10.66 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.30), residues: 738 helix: 2.94 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE E 68 TYR 0.009 0.001 TYR B 51 ARG 0.002 0.000 ARG H 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.816 Fit side-chains REVERT: A 77 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7142 (tm-30) REVERT: B 91 LYS cc_start: 0.8027 (tttp) cc_final: 0.7467 (ttmm) REVERT: C 95 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7397 (tttm) REVERT: D 38 LYS cc_start: 0.7727 (tptm) cc_final: 0.7480 (tppt) REVERT: D 46 TYR cc_start: 0.7736 (t80) cc_final: 0.6844 (t80) REVERT: D 89 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7445 (mttm) REVERT: E 66 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7566 (mp) REVERT: G 36 ARG cc_start: 0.7453 (tpp80) cc_final: 0.6928 (mmt90) REVERT: G 76 SER cc_start: 0.7985 (p) cc_final: 0.7704 (p) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.2867 time to fit residues: 28.8176 Evaluate side-chains 74 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111944 restraints weight = 14612.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109878 restraints weight = 24093.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111001 restraints weight = 21823.178| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12721 Z= 0.170 Angle : 0.509 5.659 18424 Z= 0.313 Chirality : 0.032 0.138 2107 Planarity : 0.004 0.034 1323 Dihedral : 30.542 95.709 4005 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.25 % Allowed : 10.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.30), residues: 738 helix: 3.11 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE A 68 TYR 0.009 0.001 TYR G 57 ARG 0.003 0.000 ARG H 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.04 seconds wall clock time: 30 minutes 30.83 seconds (1830.83 seconds total)