Starting phenix.real_space_refine on Thu Mar 14 18:36:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxe_26858/03_2024/7uxe_26858.pdb" } resolution = 3.38 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= 0.004 sd= 0.196 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6080 2.51 5 N 1670 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "D" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "F" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "J" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 948 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Time building chain proxies: 5.16, per 1000 atoms: 0.54 Number of scatterers: 9480 At special positions: 0 Unit cell: (118.75, 116.85, 59.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1700 8.00 N 1670 7.00 C 6080 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: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 67.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.598A pdb=" N GLY A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 39 removed outlier: 3.599A pdb=" N GLY B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.599A pdb=" N GLY C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 removed outlier: 3.597A pdb=" N GLY D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.903A pdb=" N ARG D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.598A pdb=" N GLY E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.903A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 removed outlier: 3.597A pdb=" N GLY F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 58 through 67 Processing helix chain 'F' and resid 69 through 82 Processing helix chain 'F' and resid 90 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 39 removed outlier: 3.597A pdb=" N GLY G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 50 Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'G' and resid 69 through 82 Processing helix chain 'G' and resid 90 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 removed outlier: 3.598A pdb=" N GLY H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 50 Processing helix chain 'H' and resid 58 through 67 Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'H' and resid 90 through 104 Processing helix chain 'H' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 39 removed outlier: 3.599A pdb=" N GLY I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 50 Processing helix chain 'I' and resid 58 through 67 Processing helix chain 'I' and resid 69 through 82 Processing helix chain 'I' and resid 90 through 104 Processing helix chain 'I' and resid 108 through 123 removed outlier: 3.903A pdb=" N ARG I 112 " --> pdb=" O LYS I 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 39 removed outlier: 3.597A pdb=" N GLY J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 58 through 67 Processing helix chain 'J' and resid 69 through 82 Processing helix chain 'J' and resid 90 through 104 Processing helix chain 'J' and resid 108 through 123 removed outlier: 3.904A pdb=" N ARG J 112 " --> pdb=" O LYS J 108 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3078 1.34 - 1.46: 1455 1.46 - 1.57: 5127 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 9720 Sorted by residual: bond pdb=" CA THR F 106 " pdb=" CB THR F 106 " ideal model delta sigma weight residual 1.533 1.559 -0.026 2.15e-02 2.16e+03 1.46e+00 bond pdb=" CA THR J 106 " pdb=" CB THR J 106 " ideal model delta sigma weight residual 1.533 1.559 -0.026 2.15e-02 2.16e+03 1.42e+00 bond pdb=" CA THR I 106 " pdb=" CB THR I 106 " ideal model delta sigma weight residual 1.533 1.559 -0.026 2.15e-02 2.16e+03 1.42e+00 bond pdb=" CA THR E 106 " pdb=" CB THR E 106 " ideal model delta sigma weight residual 1.533 1.559 -0.025 2.15e-02 2.16e+03 1.41e+00 bond pdb=" CA THR B 106 " pdb=" CB THR B 106 " ideal model delta sigma weight residual 1.533 1.559 -0.025 2.15e-02 2.16e+03 1.40e+00 ... (remaining 9715 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.16: 229 106.16 - 113.12: 5178 113.12 - 120.08: 3570 120.08 - 127.05: 4013 127.05 - 134.01: 150 Bond angle restraints: 13140 Sorted by residual: angle pdb=" N ILE D 125 " pdb=" CA ILE D 125 " pdb=" C ILE D 125 " ideal model delta sigma weight residual 111.77 108.23 3.54 1.04e+00 9.25e-01 1.16e+01 angle pdb=" N ILE C 125 " pdb=" CA ILE C 125 " pdb=" C ILE C 125 " ideal model delta sigma weight residual 111.77 108.24 3.53 1.04e+00 9.25e-01 1.15e+01 angle pdb=" N ILE G 125 " pdb=" CA ILE G 125 " pdb=" C ILE G 125 " ideal model delta sigma weight residual 111.77 108.25 3.52 1.04e+00 9.25e-01 1.15e+01 angle pdb=" N ILE E 125 " pdb=" CA ILE E 125 " pdb=" C ILE E 125 " ideal model delta sigma weight residual 111.77 108.26 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" N ILE H 125 " pdb=" CA ILE H 125 " pdb=" C ILE H 125 " ideal model delta sigma weight residual 111.77 108.26 3.51 1.04e+00 9.25e-01 1.14e+01 ... (remaining 13135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 4239 11.87 - 23.74: 839 23.74 - 35.61: 492 35.61 - 47.48: 187 47.48 - 59.35: 93 Dihedral angle restraints: 5850 sinusoidal: 2430 harmonic: 3420 Sorted by residual: dihedral pdb=" CA GLU C 124 " pdb=" C GLU C 124 " pdb=" N ILE C 125 " pdb=" CA ILE C 125 " ideal model delta harmonic sigma weight residual 180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU H 124 " pdb=" C GLU H 124 " pdb=" N ILE H 125 " pdb=" CA ILE H 125 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU I 124 " pdb=" C GLU I 124 " pdb=" N ILE I 125 " pdb=" CA ILE I 125 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 686 0.024 - 0.048: 387 0.048 - 0.071: 224 0.071 - 0.095: 73 0.095 - 0.119: 20 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE E 125 " pdb=" N ILE E 125 " pdb=" C ILE E 125 " pdb=" CB ILE E 125 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ILE J 125 " pdb=" N ILE J 125 " pdb=" C ILE J 125 " pdb=" CB ILE J 125 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 1387 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 106 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.24e+00 pdb=" C THR J 106 " 0.043 2.00e-02 2.50e+03 pdb=" O THR J 106 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL J 107 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 106 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C THR F 106 " 0.043 2.00e-02 2.50e+03 pdb=" O THR F 106 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL F 107 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 106 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C THR H 106 " 0.043 2.00e-02 2.50e+03 pdb=" O THR H 106 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL H 107 " -0.015 2.00e-02 2.50e+03 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 90 2.60 - 3.18: 8187 3.18 - 3.75: 14095 3.75 - 4.33: 18161 4.33 - 4.90: 30697 Nonbonded interactions: 71230 Sorted by model distance: nonbonded pdb=" O ALA C 61 " pdb=" NH2 ARG D 44 " model vdw 2.026 2.520 nonbonded pdb=" O ALA H 61 " pdb=" NH2 ARG I 44 " model vdw 2.027 2.520 nonbonded pdb=" O ALA E 61 " pdb=" NH2 ARG F 44 " model vdw 2.059 2.520 nonbonded pdb=" NH2 ARG A 44 " pdb=" O ALA J 61 " model vdw 2.071 2.520 nonbonded pdb=" O ALA B 61 " pdb=" NH2 ARG C 44 " model vdw 2.083 2.520 ... (remaining 71225 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.320 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 26.230 Find NCS groups from input model: 0.780 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.005 0.036 9720 Z= 0.293 Angle : 0.863 6.601 13140 Z= 0.519 Chirality : 0.039 0.119 1390 Planarity : 0.005 0.025 1690 Dihedral : 19.495 59.348 3610 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 2.00 % Allowed : 34.10 % Favored : 63.90 % 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: -2.79 (0.24), residues: 1130 helix: -0.30 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -5.50 (0.18), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 50 HIS 0.002 0.001 HIS I 54 PHE 0.008 0.001 PHE D 64 TYR 0.022 0.003 TYR J 40 ARG 0.009 0.001 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.140 Fit side-chains REVERT: A 54 HIS cc_start: 0.6975 (m-70) cc_final: 0.6501 (m-70) REVERT: B 38 GLN cc_start: 0.8494 (tp40) cc_final: 0.8232 (tp-100) REVERT: B 54 HIS cc_start: 0.7007 (m-70) cc_final: 0.6580 (m-70) REVERT: B 77 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7612 (tttp) REVERT: D 38 GLN cc_start: 0.8546 (tp40) cc_final: 0.8228 (tp-100) REVERT: D 54 HIS cc_start: 0.7001 (m-70) cc_final: 0.6531 (m-70) REVERT: D 77 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7719 (ttmm) REVERT: F 54 HIS cc_start: 0.7045 (m-70) cc_final: 0.6580 (m-70) REVERT: G 38 GLN cc_start: 0.8473 (tp40) cc_final: 0.8220 (tp-100) REVERT: G 54 HIS cc_start: 0.7002 (m-70) cc_final: 0.6580 (m-70) REVERT: I 38 GLN cc_start: 0.8437 (tp40) cc_final: 0.8198 (tp40) REVERT: I 54 HIS cc_start: 0.6948 (m-70) cc_final: 0.6474 (m-70) REVERT: I 77 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7637 (ttmm) REVERT: I 101 MET cc_start: 0.8789 (ttp) cc_final: 0.8579 (ttp) REVERT: J 54 HIS cc_start: 0.6827 (m-70) cc_final: 0.6495 (m-70) outliers start: 20 outliers final: 0 residues processed: 231 average time/residue: 0.3241 time to fit residues: 93.2620 Evaluate side-chains 193 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0010 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 10.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9720 Z= 0.281 Angle : 0.673 4.541 13140 Z= 0.363 Chirality : 0.039 0.102 1390 Planarity : 0.005 0.024 1690 Dihedral : 5.277 16.742 1260 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.02 % Favored : 83.98 % Rotamer: Outliers : 6.10 % Allowed : 27.20 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.24), residues: 1130 helix: 0.41 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.34 (0.22), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.003 0.001 HIS C 54 PHE 0.016 0.001 PHE E 64 TYR 0.016 0.002 TYR C 40 ARG 0.003 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 210 time to evaluate : 1.114 Fit side-chains REVERT: A 54 HIS cc_start: 0.6953 (m-70) cc_final: 0.6634 (m-70) REVERT: A 122 LEU cc_start: 0.8540 (mt) cc_final: 0.8295 (tt) REVERT: B 54 HIS cc_start: 0.6942 (m-70) cc_final: 0.6682 (m-70) REVERT: B 62 ARG cc_start: 0.8571 (tpt170) cc_final: 0.8356 (tpt170) REVERT: B 73 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6942 (mtm180) REVERT: B 77 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7560 (tttp) REVERT: B 122 LEU cc_start: 0.8569 (mt) cc_final: 0.8219 (tt) REVERT: C 54 HIS cc_start: 0.6726 (m-70) cc_final: 0.6500 (m-70) REVERT: C 122 LEU cc_start: 0.8749 (mt) cc_final: 0.8287 (tt) REVERT: D 54 HIS cc_start: 0.7024 (m-70) cc_final: 0.6608 (m-70) REVERT: D 77 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7863 (ttmm) REVERT: E 38 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8104 (tp-100) REVERT: E 122 LEU cc_start: 0.8502 (mt) cc_final: 0.8264 (tt) REVERT: F 54 HIS cc_start: 0.6945 (m-70) cc_final: 0.6630 (m-70) REVERT: F 73 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7046 (mtm180) REVERT: F 122 LEU cc_start: 0.8542 (mt) cc_final: 0.8314 (tt) REVERT: G 54 HIS cc_start: 0.6951 (m-70) cc_final: 0.6701 (m-70) REVERT: G 62 ARG cc_start: 0.8591 (tpt170) cc_final: 0.8378 (tpt170) REVERT: G 73 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6965 (mtm180) REVERT: G 122 LEU cc_start: 0.8553 (mt) cc_final: 0.8187 (tt) REVERT: H 54 HIS cc_start: 0.6688 (m170) cc_final: 0.6486 (m-70) REVERT: H 122 LEU cc_start: 0.8738 (mt) cc_final: 0.8290 (tt) REVERT: I 54 HIS cc_start: 0.6959 (m-70) cc_final: 0.6567 (m-70) REVERT: I 77 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7675 (ttmm) REVERT: J 38 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8125 (tp-100) REVERT: J 54 HIS cc_start: 0.6817 (m-70) cc_final: 0.6540 (m-70) REVERT: J 122 LEU cc_start: 0.8508 (mt) cc_final: 0.8244 (tt) outliers start: 61 outliers final: 24 residues processed: 256 average time/residue: 0.3062 time to fit residues: 98.5940 Evaluate side-chains 220 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7588 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9720 Z= 0.210 Angle : 0.614 5.512 13140 Z= 0.331 Chirality : 0.037 0.112 1390 Planarity : 0.004 0.024 1690 Dihedral : 5.113 16.141 1260 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer: Outliers : 4.50 % Allowed : 28.80 % Favored : 66.70 % 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: -1.14 (0.25), residues: 1130 helix: 1.01 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.36 (0.21), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 50 HIS 0.002 0.001 HIS B 96 PHE 0.015 0.001 PHE B 64 TYR 0.019 0.002 TYR C 40 ARG 0.002 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 1.138 Fit side-chains REVERT: A 54 HIS cc_start: 0.6962 (m-70) cc_final: 0.6639 (m-70) REVERT: A 73 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7005 (mtm180) REVERT: A 122 LEU cc_start: 0.8614 (mt) cc_final: 0.8345 (tt) REVERT: B 73 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6910 (mtm180) REVERT: B 77 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7601 (tttp) REVERT: B 122 LEU cc_start: 0.8590 (mt) cc_final: 0.8246 (tt) REVERT: C 73 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7005 (mtm180) REVERT: C 122 LEU cc_start: 0.8708 (mt) cc_final: 0.8259 (tt) REVERT: D 54 HIS cc_start: 0.7027 (m-70) cc_final: 0.6666 (m-70) REVERT: D 77 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7862 (ttmm) REVERT: E 122 LEU cc_start: 0.8606 (mt) cc_final: 0.8278 (tt) REVERT: F 54 HIS cc_start: 0.6972 (m-70) cc_final: 0.6651 (m-70) REVERT: F 122 LEU cc_start: 0.8554 (mt) cc_final: 0.8319 (tt) REVERT: G 122 LEU cc_start: 0.8611 (mt) cc_final: 0.8265 (tt) REVERT: H 73 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7004 (mtm180) REVERT: H 122 LEU cc_start: 0.8699 (mt) cc_final: 0.8261 (tt) REVERT: I 54 HIS cc_start: 0.6945 (m-70) cc_final: 0.6583 (m-70) REVERT: I 77 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7788 (ttmm) REVERT: J 122 LEU cc_start: 0.8622 (mt) cc_final: 0.8270 (tt) outliers start: 45 outliers final: 28 residues processed: 212 average time/residue: 0.2637 time to fit residues: 72.9760 Evaluate side-chains 221 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.0010 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9720 Z= 0.184 Angle : 0.596 5.855 13140 Z= 0.321 Chirality : 0.037 0.158 1390 Planarity : 0.004 0.029 1690 Dihedral : 4.912 15.735 1260 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Rotamer: Outliers : 5.40 % Allowed : 27.30 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1130 helix: 1.37 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.35 (0.21), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 50 HIS 0.002 0.000 HIS E 54 PHE 0.016 0.001 PHE B 64 TYR 0.017 0.002 TYR H 40 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 187 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.5925 (t70) cc_final: 0.5683 (t70) REVERT: A 73 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6918 (mtm180) REVERT: A 122 LEU cc_start: 0.8584 (mt) cc_final: 0.8333 (tt) REVERT: B 77 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7599 (tttp) REVERT: B 122 LEU cc_start: 0.8589 (mt) cc_final: 0.8300 (tt) REVERT: C 73 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6997 (mtm180) REVERT: C 122 LEU cc_start: 0.8650 (mt) cc_final: 0.8254 (tt) REVERT: D 54 HIS cc_start: 0.6977 (m-70) cc_final: 0.6587 (m-70) REVERT: D 55 MET cc_start: 0.7221 (mmm) cc_final: 0.6937 (mmp) REVERT: D 77 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7811 (ttmm) REVERT: E 122 LEU cc_start: 0.8572 (mt) cc_final: 0.8333 (tt) REVERT: F 81 ASN cc_start: 0.8975 (m-40) cc_final: 0.8769 (m-40) REVERT: F 122 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (tt) REVERT: G 122 LEU cc_start: 0.8583 (mt) cc_final: 0.8276 (tt) REVERT: H 73 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7050 (mtm180) REVERT: H 122 LEU cc_start: 0.8623 (mt) cc_final: 0.8235 (tt) REVERT: I 54 HIS cc_start: 0.6887 (m-70) cc_final: 0.6552 (m-70) REVERT: I 55 MET cc_start: 0.7219 (mmm) cc_final: 0.6933 (mmp) REVERT: I 77 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7622 (ttmm) REVERT: J 122 LEU cc_start: 0.8586 (mt) cc_final: 0.8321 (tt) outliers start: 54 outliers final: 33 residues processed: 225 average time/residue: 0.2443 time to fit residues: 72.6480 Evaluate side-chains 216 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 127 PHE Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 127 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9720 Z= 0.302 Angle : 0.656 5.923 13140 Z= 0.351 Chirality : 0.041 0.162 1390 Planarity : 0.004 0.031 1690 Dihedral : 4.991 15.632 1260 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.02 % Favored : 83.98 % Rotamer: Outliers : 6.10 % Allowed : 27.20 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1130 helix: 1.40 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.22 (0.24), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 50 HIS 0.002 0.000 HIS H 54 PHE 0.019 0.002 PHE B 64 TYR 0.016 0.002 TYR C 40 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 182 time to evaluate : 1.172 Fit side-chains REVERT: A 18 ASP cc_start: 0.6649 (t70) cc_final: 0.6246 (t0) REVERT: A 73 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6876 (mtm180) REVERT: A 109 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: A 122 LEU cc_start: 0.8615 (mt) cc_final: 0.8388 (tt) REVERT: B 55 MET cc_start: 0.7153 (mmm) cc_final: 0.6728 (mmp) REVERT: B 73 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6987 (mtm180) REVERT: B 77 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7603 (ttmm) REVERT: B 122 LEU cc_start: 0.8664 (mt) cc_final: 0.8310 (tt) REVERT: C 73 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7086 (mtm180) REVERT: C 122 LEU cc_start: 0.8776 (mt) cc_final: 0.8323 (tt) REVERT: D 54 HIS cc_start: 0.6996 (m-70) cc_final: 0.6614 (m-70) REVERT: D 55 MET cc_start: 0.7302 (mmm) cc_final: 0.7092 (mmp) REVERT: D 73 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6923 (mtm180) REVERT: D 77 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7796 (ttmm) REVERT: E 122 LEU cc_start: 0.8643 (mt) cc_final: 0.8366 (tt) REVERT: F 122 LEU cc_start: 0.8616 (mt) cc_final: 0.8394 (tt) REVERT: G 55 MET cc_start: 0.7121 (mmm) cc_final: 0.6702 (mmp) REVERT: G 73 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7000 (mtm180) REVERT: G 122 LEU cc_start: 0.8662 (mt) cc_final: 0.8296 (tt) REVERT: H 73 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7088 (mtm180) REVERT: H 122 LEU cc_start: 0.8757 (mt) cc_final: 0.8307 (tt) REVERT: I 77 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7801 (ttmm) REVERT: J 122 LEU cc_start: 0.8669 (mt) cc_final: 0.8376 (tt) outliers start: 61 outliers final: 28 residues processed: 225 average time/residue: 0.2815 time to fit residues: 81.3030 Evaluate side-chains 215 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9720 Z= 0.175 Angle : 0.595 6.501 13140 Z= 0.323 Chirality : 0.038 0.188 1390 Planarity : 0.004 0.029 1690 Dihedral : 4.793 15.394 1260 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 5.50 % Allowed : 26.20 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1130 helix: 1.68 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.25 (0.23), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.002 0.000 HIS E 54 PHE 0.015 0.001 PHE G 64 TYR 0.019 0.001 TYR C 40 ARG 0.004 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 1.050 Fit side-chains REVERT: A 18 ASP cc_start: 0.6502 (t70) cc_final: 0.6148 (t70) REVERT: A 73 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6827 (mtm180) REVERT: A 109 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 122 LEU cc_start: 0.8640 (mt) cc_final: 0.8387 (tt) REVERT: B 73 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6968 (mtm180) REVERT: B 77 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7610 (ttmm) REVERT: B 122 LEU cc_start: 0.8580 (mt) cc_final: 0.8308 (tt) REVERT: C 55 MET cc_start: 0.6952 (mmm) cc_final: 0.6645 (mmp) REVERT: C 109 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: C 122 LEU cc_start: 0.8626 (mt) cc_final: 0.8276 (tt) REVERT: D 54 HIS cc_start: 0.7037 (m-70) cc_final: 0.6628 (m-70) REVERT: D 55 MET cc_start: 0.7412 (mmm) cc_final: 0.7196 (mmp) REVERT: D 73 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6869 (mtm180) REVERT: D 77 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7836 (ttmm) REVERT: F 122 LEU cc_start: 0.8632 (mt) cc_final: 0.8392 (tt) REVERT: G 122 LEU cc_start: 0.8582 (mt) cc_final: 0.8294 (tt) REVERT: H 55 MET cc_start: 0.7098 (mmm) cc_final: 0.6813 (mmp) REVERT: H 109 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: H 122 LEU cc_start: 0.8667 (mt) cc_final: 0.8316 (tt) REVERT: I 55 MET cc_start: 0.7161 (mmm) cc_final: 0.6824 (mmp) REVERT: I 73 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6927 (mtm180) REVERT: I 77 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7765 (ttmm) outliers start: 55 outliers final: 33 residues processed: 224 average time/residue: 0.2859 time to fit residues: 82.9024 Evaluate side-chains 219 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 127 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9720 Z= 0.246 Angle : 0.636 7.065 13140 Z= 0.342 Chirality : 0.042 0.213 1390 Planarity : 0.004 0.030 1690 Dihedral : 4.700 15.288 1260 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 4.90 % Allowed : 25.00 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1130 helix: 1.78 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.13 (0.24), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 50 HIS 0.003 0.001 HIS J 96 PHE 0.007 0.001 PHE E 64 TYR 0.008 0.001 TYR H 40 ARG 0.004 0.000 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 182 time to evaluate : 1.200 Fit side-chains REVERT: A 18 ASP cc_start: 0.6779 (t70) cc_final: 0.6322 (t0) REVERT: A 73 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6859 (mtm180) REVERT: A 109 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: A 122 LEU cc_start: 0.8727 (mt) cc_final: 0.8457 (tt) REVERT: B 55 MET cc_start: 0.7133 (mmm) cc_final: 0.6713 (mmp) REVERT: B 73 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6992 (mtm180) REVERT: B 122 LEU cc_start: 0.8598 (mt) cc_final: 0.8308 (tt) REVERT: C 73 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7064 (mtm180) REVERT: C 122 LEU cc_start: 0.8721 (mt) cc_final: 0.8321 (tt) REVERT: D 73 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6916 (mtm180) REVERT: D 77 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7778 (ttmm) REVERT: F 73 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6982 (mtm180) REVERT: F 122 LEU cc_start: 0.8712 (mt) cc_final: 0.8405 (tt) REVERT: G 55 MET cc_start: 0.7114 (mmm) cc_final: 0.6707 (mmp) REVERT: G 122 LEU cc_start: 0.8626 (mt) cc_final: 0.8305 (tt) REVERT: H 73 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7057 (mtm180) REVERT: H 122 LEU cc_start: 0.8711 (mt) cc_final: 0.8310 (tt) REVERT: I 55 MET cc_start: 0.7230 (mmm) cc_final: 0.6921 (mmp) REVERT: I 73 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6932 (mtm180) REVERT: I 77 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7743 (ttmm) outliers start: 49 outliers final: 31 residues processed: 214 average time/residue: 0.2728 time to fit residues: 75.7466 Evaluate side-chains 220 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9720 Z= 0.229 Angle : 0.643 7.740 13140 Z= 0.344 Chirality : 0.041 0.227 1390 Planarity : 0.004 0.032 1690 Dihedral : 4.766 15.986 1260 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer: Outliers : 4.70 % Allowed : 25.50 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1130 helix: 1.74 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -5.02 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 43 HIS 0.002 0.001 HIS E 54 PHE 0.007 0.001 PHE C 64 TYR 0.010 0.001 TYR C 40 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.139 Fit side-chains REVERT: A 18 ASP cc_start: 0.6864 (t70) cc_final: 0.6364 (t0) REVERT: A 73 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6840 (mtm180) REVERT: A 109 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: A 122 LEU cc_start: 0.8676 (mt) cc_final: 0.8442 (tt) REVERT: B 55 MET cc_start: 0.7350 (mmm) cc_final: 0.6997 (mmp) REVERT: B 73 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6980 (mtm180) REVERT: B 122 LEU cc_start: 0.8609 (mt) cc_final: 0.8345 (tt) REVERT: C 55 MET cc_start: 0.6916 (mmm) cc_final: 0.6664 (mmp) REVERT: C 73 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: C 122 LEU cc_start: 0.8649 (mt) cc_final: 0.8338 (tt) REVERT: D 55 MET cc_start: 0.7138 (mmm) cc_final: 0.6783 (mmp) REVERT: D 73 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6911 (mtm180) REVERT: D 77 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7782 (ttmm) REVERT: F 73 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6968 (mtm180) REVERT: F 122 LEU cc_start: 0.8643 (mt) cc_final: 0.8431 (tt) REVERT: G 55 MET cc_start: 0.7344 (mmm) cc_final: 0.6984 (mmp) REVERT: G 73 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6994 (mtm180) REVERT: G 122 LEU cc_start: 0.8604 (mt) cc_final: 0.8316 (tt) REVERT: H 55 MET cc_start: 0.6931 (mmm) cc_final: 0.6680 (mmp) REVERT: H 73 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: H 122 LEU cc_start: 0.8651 (mt) cc_final: 0.8290 (tt) REVERT: I 55 MET cc_start: 0.7308 (mmm) cc_final: 0.7030 (mmp) REVERT: I 73 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6871 (mtm180) outliers start: 47 outliers final: 30 residues processed: 213 average time/residue: 0.3005 time to fit residues: 81.3154 Evaluate side-chains 219 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9720 Z= 0.223 Angle : 0.635 8.004 13140 Z= 0.340 Chirality : 0.042 0.246 1390 Planarity : 0.004 0.031 1690 Dihedral : 4.683 16.627 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % Rotamer: Outliers : 4.30 % Allowed : 26.00 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1130 helix: 1.75 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -4.94 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 43 HIS 0.002 0.001 HIS A 96 PHE 0.006 0.001 PHE H 21 TYR 0.009 0.001 TYR C 40 ARG 0.002 0.000 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 1.059 Fit side-chains REVERT: A 18 ASP cc_start: 0.7277 (t70) cc_final: 0.6644 (t0) REVERT: A 73 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: A 109 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: A 122 LEU cc_start: 0.8652 (mt) cc_final: 0.8397 (tt) REVERT: B 55 MET cc_start: 0.7425 (mmm) cc_final: 0.7157 (mmp) REVERT: B 73 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6976 (mtm180) REVERT: B 122 LEU cc_start: 0.8593 (mt) cc_final: 0.8350 (tt) REVERT: C 73 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: C 122 LEU cc_start: 0.8641 (mt) cc_final: 0.8304 (tt) REVERT: D 55 MET cc_start: 0.7239 (mmm) cc_final: 0.6907 (mmp) REVERT: D 73 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6901 (mtm110) REVERT: F 73 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6973 (mtm180) REVERT: F 122 LEU cc_start: 0.8653 (mt) cc_final: 0.8404 (tt) REVERT: G 73 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6985 (mtm180) REVERT: G 122 LEU cc_start: 0.8619 (mt) cc_final: 0.8334 (tt) REVERT: H 73 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: H 122 LEU cc_start: 0.8620 (mt) cc_final: 0.8286 (tt) REVERT: I 55 MET cc_start: 0.7375 (mmm) cc_final: 0.7130 (mmp) REVERT: I 73 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6893 (mtm110) outliers start: 43 outliers final: 30 residues processed: 210 average time/residue: 0.3127 time to fit residues: 82.7414 Evaluate side-chains 219 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9720 Z= 0.180 Angle : 0.634 8.467 13140 Z= 0.338 Chirality : 0.039 0.213 1390 Planarity : 0.004 0.031 1690 Dihedral : 4.539 17.205 1260 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer: Outliers : 3.00 % Allowed : 27.30 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1130 helix: 1.81 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -4.88 (0.24), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 43 HIS 0.002 0.000 HIS J 54 PHE 0.006 0.001 PHE I 21 TYR 0.008 0.001 TYR D 40 ARG 0.003 0.000 ARG C 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.140 Fit side-chains REVERT: A 18 ASP cc_start: 0.7347 (t70) cc_final: 0.6857 (t70) REVERT: A 54 HIS cc_start: 0.7109 (m-70) cc_final: 0.6890 (m-70) REVERT: A 73 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6867 (mtp180) REVERT: B 73 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: C 55 MET cc_start: 0.7007 (mmm) cc_final: 0.6769 (mmp) REVERT: C 122 LEU cc_start: 0.8521 (mt) cc_final: 0.8300 (tt) REVERT: D 55 MET cc_start: 0.7236 (mmm) cc_final: 0.6900 (mmp) REVERT: E 55 MET cc_start: 0.6843 (mmm) cc_final: 0.6537 (mmp) REVERT: G 55 MET cc_start: 0.7042 (mmm) cc_final: 0.6674 (mmp) REVERT: G 122 LEU cc_start: 0.8618 (mt) cc_final: 0.8357 (tt) REVERT: H 55 MET cc_start: 0.7033 (mmm) cc_final: 0.6797 (mmp) REVERT: H 122 LEU cc_start: 0.8560 (mt) cc_final: 0.8323 (tt) REVERT: I 55 MET cc_start: 0.7401 (mmm) cc_final: 0.7151 (mmp) REVERT: J 55 MET cc_start: 0.6453 (mmm) cc_final: 0.6071 (mmp) outliers start: 30 outliers final: 26 residues processed: 209 average time/residue: 0.2867 time to fit residues: 76.7244 Evaluate side-chains 207 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain J residue 90 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119723 restraints weight = 10919.427| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.97 r_work: 0.3197 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9720 Z= 0.284 Angle : 0.686 8.252 13140 Z= 0.363 Chirality : 0.044 0.263 1390 Planarity : 0.004 0.032 1690 Dihedral : 4.657 17.541 1260 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 3.50 % Allowed : 27.30 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1130 helix: 1.70 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -4.82 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.003 0.001 HIS F 96 PHE 0.008 0.001 PHE H 64 TYR 0.009 0.001 TYR D 40 ARG 0.002 0.000 ARG J 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.91 seconds wall clock time: 39 minutes 53.51 seconds (2393.51 seconds total)