Starting phenix.real_space_refine on Fri Mar 15 14:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/03_2024/7wlr_32591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/03_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_32591/03_2024/7wlr_32591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/03_2024/7wlr_32591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/03_2024/7wlr_32591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlr_32591/03_2024/7wlr_32591.pdb" } 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 Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 75": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.56, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.63 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: 4.14 Time building geometry restraints manager: 7.14 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: 97.95 - 104.87: 1184 104.87 - 111.79: 6702 111.79 - 118.72: 3436 118.72 - 125.64: 6104 125.64 - 132.56: 998 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 2.440 nonbonded pdb=" OG SER H 94 " pdb=" OE1 GLU H 97 " model vdw 2.346 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.365 2.440 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.383 2.440 ... (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 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: 0.410 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: 0.000 Extract box with map and model: 1.950 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 41.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.740 ------------------------------------------------------------------------------- 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 : 0.940 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: 0.3728 time to fit residues: 50.4993 Evaluate side-chains 62 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7220 moved from start: 0.1517 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= 0.185 Angle : 0.546 6.202 18424 Z= 0.335 Chirality : 0.033 0.145 2107 Planarity : 0.004 0.042 1323 Dihedral : 31.293 93.218 4005 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.78 % Allowed : 5.33 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.30), residues: 738 helix: 2.60 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (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 H 74 TYR 0.011 0.001 TYR G 57 ARG 0.005 0.001 ARG B 78 *********************** 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 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.923 Fit side-chains REVERT: A 77 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7264 (tm-30) REVERT: B 91 LYS cc_start: 0.7857 (tttp) cc_final: 0.7260 (ttmm) REVERT: C 41 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7535 (mt0) REVERT: C 95 LYS cc_start: 0.7543 (ttmt) cc_final: 0.7245 (tttm) REVERT: D 46 TYR cc_start: 0.7672 (t80) cc_final: 0.6811 (t80) REVERT: D 75 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6906 (tm-30) REVERT: D 89 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7366 (mttm) REVERT: G 36 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6641 (mmt90) REVERT: G 107 VAL cc_start: 0.8887 (p) cc_final: 0.8641 (m) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.3071 time to fit residues: 30.4962 Evaluate side-chains 66 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 76 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0000 chunk 28 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12721 Z= 0.217 Angle : 0.549 6.750 18424 Z= 0.334 Chirality : 0.034 0.142 2107 Planarity : 0.004 0.037 1323 Dihedral : 31.064 96.634 4005 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 7.68 % Favored : 91.22 % 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: 2.82 (0.30), residues: 738 helix: 2.67 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE G 25 TYR 0.010 0.001 TYR G 57 ARG 0.007 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 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.818 Fit side-chains REVERT: A 77 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 91 LYS cc_start: 0.7992 (tttp) cc_final: 0.7402 (ttmm) REVERT: C 95 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7382 (tttm) REVERT: D 46 TYR cc_start: 0.7735 (t80) cc_final: 0.6973 (t80) REVERT: D 66 MET cc_start: 0.8595 (mmm) cc_final: 0.8317 (mmm) REVERT: D 89 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7442 (mttm) REVERT: G 14 SER cc_start: 0.4913 (m) cc_final: 0.4709 (t) REVERT: G 36 ARG cc_start: 0.7029 (tpp80) cc_final: 0.6552 (mmt90) REVERT: H 38 LYS cc_start: 0.7081 (tppt) cc_final: 0.6289 (mtpt) REVERT: H 39 GLU cc_start: 0.7822 (pt0) cc_final: 0.7328 (mm-30) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.3053 time to fit residues: 34.6487 Evaluate side-chains 73 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12721 Z= 0.347 Angle : 0.623 9.642 18424 Z= 0.368 Chirality : 0.038 0.145 2107 Planarity : 0.005 0.040 1323 Dihedral : 31.227 102.012 4005 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.19 % Allowed : 9.72 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.30), residues: 738 helix: 2.38 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.20 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.011 0.002 PHE G 25 TYR 0.015 0.002 TYR B 51 ARG 0.007 0.001 ARG H 120 *********************** 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 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.895 Fit side-chains REVERT: A 77 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 91 LYS cc_start: 0.8060 (tttp) cc_final: 0.7472 (ttmm) REVERT: C 95 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7485 (tttm) REVERT: D 38 LYS cc_start: 0.7901 (tptm) cc_final: 0.7410 (tppt) REVERT: D 46 TYR cc_start: 0.7785 (t80) cc_final: 0.7130 (t80) REVERT: D 89 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7406 (mttm) REVERT: G 36 ARG cc_start: 0.7494 (tpp80) cc_final: 0.6881 (mmt90) REVERT: H 39 GLU cc_start: 0.8141 (pt0) cc_final: 0.7641 (mm-30) REVERT: H 75 GLU cc_start: 0.7350 (tp30) cc_final: 0.6720 (mt-10) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.2783 time to fit residues: 32.1037 Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3527 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= 0.228 Angle : 0.546 5.374 18424 Z= 0.333 Chirality : 0.034 0.134 2107 Planarity : 0.004 0.039 1323 Dihedral : 30.891 101.559 4005 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.94 % Allowed : 11.91 % Favored : 87.15 % 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: 2.69 (0.30), residues: 738 helix: 2.70 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 68 TYR 0.010 0.001 TYR G 57 ARG 0.004 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 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.947 Fit side-chains REVERT: A 77 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 91 LYS cc_start: 0.8002 (tttp) cc_final: 0.7422 (ttmm) REVERT: C 95 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7488 (tttm) REVERT: D 38 LYS cc_start: 0.7740 (tptm) cc_final: 0.7296 (tppt) REVERT: D 46 TYR cc_start: 0.7724 (t80) cc_final: 0.6928 (t80) REVERT: D 63 MET cc_start: 0.8618 (tpp) cc_final: 0.8372 (tpp) REVERT: D 89 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7427 (mttm) REVERT: E 62 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (mm) REVERT: G 36 ARG cc_start: 0.7473 (tpp80) cc_final: 0.6929 (mmt90) REVERT: G 61 GLU cc_start: 0.7561 (tp30) cc_final: 0.7126 (tt0) REVERT: H 38 LYS cc_start: 0.7114 (tppt) cc_final: 0.6581 (mtpt) REVERT: H 39 GLU cc_start: 0.8121 (pt0) cc_final: 0.7638 (mm-30) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.2853 time to fit residues: 30.7113 Evaluate side-chains 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7316 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12721 Z= 0.165 Angle : 0.526 5.443 18424 Z= 0.324 Chirality : 0.033 0.128 2107 Planarity : 0.004 0.035 1323 Dihedral : 30.855 101.573 4005 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.41 % Allowed : 11.76 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.30), residues: 738 helix: 2.94 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 53 PHE 0.006 0.001 PHE E 68 TYR 0.008 0.001 TYR B 51 ARG 0.005 0.000 ARG D 96 *********************** 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 82 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.981 Fit side-chains REVERT: A 77 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 91 LYS cc_start: 0.7990 (tttp) cc_final: 0.7415 (ttmm) REVERT: C 95 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7458 (tttm) REVERT: D 38 LYS cc_start: 0.7724 (tptm) cc_final: 0.7299 (tppt) REVERT: D 46 TYR cc_start: 0.7665 (t80) cc_final: 0.6877 (t80) REVERT: D 89 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7403 (mttm) REVERT: G 36 ARG cc_start: 0.7450 (tpp80) cc_final: 0.6941 (mmt90) REVERT: G 61 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: H 38 LYS cc_start: 0.7247 (tppt) cc_final: 0.6584 (mtpt) REVERT: H 39 GLU cc_start: 0.8097 (pt0) cc_final: 0.7637 (mm-30) REVERT: H 88 ASN cc_start: 0.8339 (m110) cc_final: 0.7816 (m110) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.2756 time to fit residues: 29.5803 Evaluate side-chains 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3619 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= 0.183 Angle : 0.524 5.119 18424 Z= 0.322 Chirality : 0.033 0.132 2107 Planarity : 0.004 0.035 1323 Dihedral : 30.807 100.435 4005 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.51 % Allowed : 10.03 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.30), residues: 738 helix: 3.01 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 68 TYR 0.011 0.001 TYR G 57 ARG 0.004 0.000 ARG H 120 *********************** 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 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.920 Fit side-chains REVERT: A 77 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 91 LYS cc_start: 0.8002 (tttp) cc_final: 0.7423 (ttmm) REVERT: C 95 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7430 (tttm) REVERT: D 38 LYS cc_start: 0.7734 (tptm) cc_final: 0.7336 (tppt) REVERT: D 46 TYR cc_start: 0.7724 (t80) cc_final: 0.6843 (t80) REVERT: D 89 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7388 (mttm) REVERT: E 66 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7646 (mp) REVERT: G 36 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6948 (mmt90) REVERT: G 61 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: H 38 LYS cc_start: 0.7288 (tppt) cc_final: 0.6714 (mtpt) REVERT: H 39 GLU cc_start: 0.8138 (pt0) cc_final: 0.7631 (mm-30) REVERT: H 88 ASN cc_start: 0.8284 (m110) cc_final: 0.7821 (m110) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.2634 time to fit residues: 30.7288 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12721 Z= 0.393 Angle : 0.628 9.808 18424 Z= 0.369 Chirality : 0.038 0.147 2107 Planarity : 0.005 0.042 1323 Dihedral : 31.250 105.281 4005 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.98 % Allowed : 10.19 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.30), residues: 738 helix: 2.48 (0.21), residues: 551 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.009 0.002 PHE H 69 TYR 0.014 0.002 TYR B 51 ARG 0.003 0.001 ARG A 117 *********************** 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 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.916 Fit side-chains REVERT: A 77 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 91 LYS cc_start: 0.8125 (tttp) cc_final: 0.7506 (ttmm) REVERT: C 95 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7459 (tttm) REVERT: D 38 LYS cc_start: 0.7856 (tptm) cc_final: 0.7452 (tppt) REVERT: D 46 TYR cc_start: 0.7848 (t80) cc_final: 0.7139 (t80) REVERT: D 89 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7445 (mttm) REVERT: E 66 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7691 (mm) REVERT: G 36 ARG cc_start: 0.7403 (tpp80) cc_final: 0.6905 (mmt90) REVERT: G 61 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: H 39 GLU cc_start: 0.8166 (pt0) cc_final: 0.7697 (mm-30) REVERT: H 75 GLU cc_start: 0.7373 (tp30) cc_final: 0.6797 (mt-10) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.2552 time to fit residues: 29.7560 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 76 SER 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: 0.9990 chunk 70 optimal weight: 2.9990 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: 0.9980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12721 Z= 0.176 Angle : 0.522 7.065 18424 Z= 0.320 Chirality : 0.033 0.129 2107 Planarity : 0.004 0.039 1323 Dihedral : 30.674 101.521 4005 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.57 % Allowed : 11.60 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.31), residues: 738 helix: 3.03 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.20 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE A 68 TYR 0.009 0.001 TYR G 57 ARG 0.008 0.000 ARG D 96 *********************** 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 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.906 Fit side-chains REVERT: A 77 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 91 LYS cc_start: 0.8000 (tttp) cc_final: 0.7417 (ttmm) REVERT: C 95 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7399 (tttm) REVERT: D 38 LYS cc_start: 0.7723 (tptm) cc_final: 0.7372 (tppt) REVERT: D 46 TYR cc_start: 0.7713 (t80) cc_final: 0.6792 (t80) REVERT: D 89 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7423 (mttm) REVERT: E 66 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7551 (mp) REVERT: G 36 ARG cc_start: 0.7360 (tpp80) cc_final: 0.6908 (mmt90) REVERT: G 61 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: H 38 LYS cc_start: 0.7602 (tptt) cc_final: 0.6894 (mtpt) REVERT: H 39 GLU cc_start: 0.8137 (pt0) cc_final: 0.7666 (mm-30) REVERT: H 88 ASN cc_start: 0.8148 (m110) cc_final: 0.7691 (m110) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.2806 time to fit residues: 30.9632 Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12721 Z= 0.229 Angle : 0.537 6.536 18424 Z= 0.326 Chirality : 0.034 0.137 2107 Planarity : 0.004 0.039 1323 Dihedral : 30.815 102.135 4005 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.41 % Allowed : 11.76 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.31), residues: 738 helix: 2.96 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 68 TYR 0.009 0.001 TYR G 57 ARG 0.004 0.000 ARG D 96 ********************** 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 82 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.925 Fit side-chains REVERT: A 77 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 130 ARG cc_start: 0.7826 (tmt170) cc_final: 0.7230 (ttm170) REVERT: B 91 LYS cc_start: 0.8072 (tttp) cc_final: 0.7473 (ttmm) REVERT: C 95 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7421 (tttm) REVERT: D 38 LYS cc_start: 0.7791 (tptm) cc_final: 0.7430 (tppt) REVERT: D 46 TYR cc_start: 0.7736 (t80) cc_final: 0.6828 (t80) REVERT: D 89 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7423 (mttm) REVERT: E 66 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7667 (mp) REVERT: G 36 ARG cc_start: 0.7393 (tpp80) cc_final: 0.6909 (mmt90) REVERT: G 61 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: H 38 LYS cc_start: 0.7585 (tptt) cc_final: 0.6896 (mtpt) REVERT: H 39 GLU cc_start: 0.8113 (pt0) cc_final: 0.7648 (mm-30) REVERT: H 88 ASN cc_start: 0.8279 (m110) cc_final: 0.7804 (m110) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.2819 time to fit residues: 30.4970 Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120409 restraints weight = 14912.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119213 restraints weight = 23131.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120090 restraints weight = 23593.263| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12721 Z= 0.161 Angle : 0.506 5.136 18424 Z= 0.312 Chirality : 0.032 0.126 2107 Planarity : 0.004 0.040 1323 Dihedral : 30.583 99.667 4005 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.10 % Allowed : 12.07 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.31), residues: 738 helix: 3.17 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 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: 1665.23 seconds wall clock time: 31 minutes 8.28 seconds (1868.28 seconds total)