Starting phenix.real_space_refine on Wed Jan 17 22:33:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyi_15024/01_2024/7zyi_15024_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 S 46 5.16 5 Na 2 4.78 5 C 4286 2.51 5 N 1075 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6641 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2248 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' NA': 2, 'CHO': 2, 'CLR': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 4.66, per 1000 atoms: 0.70 Number of scatterers: 6641 At special positions: 0 Unit cell: (118.8, 116.82, 89.1, 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 46 16.00 Na 2 11.00 O 1232 8.00 N 1075 7.00 C 4286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 2.41 Conformation dependent library (CDL) restraints added in 1.6 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 12 sheets defined 30.0% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 removed outlier: 4.230A pdb=" N CYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 116 through 141 removed outlier: 4.098A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 181 through 212 removed outlier: 4.340A pdb=" N ARG A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 285 through 309 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.636A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.635A pdb=" N VAL H 182 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.599A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.932A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.107A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'L' and resid 85 through 90 removed outlier: 3.601A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.636A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 144 through 150 removed outlier: 3.711A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.902A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 23 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.659A pdb=" N THR K 110 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 758 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: 1.95 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1028 1.31 - 1.43: 1856 1.43 - 1.56: 3825 1.56 - 1.69: 19 1.69 - 1.81: 71 Bond restraints: 6799 Sorted by residual: bond pdb=" C12 CHO A 702 " pdb=" C13 CHO A 702 " ideal model delta sigma weight residual 1.529 1.198 0.331 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C12 CHO A 703 " pdb=" C13 CHO A 703 " ideal model delta sigma weight residual 1.529 1.202 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C13 CHO A 702 " pdb=" C17 CHO A 702 " ideal model delta sigma weight residual 1.549 1.234 0.315 2.00e-02 2.50e+03 2.49e+02 bond pdb=" C13 CHO A 703 " pdb=" C17 CHO A 703 " ideal model delta sigma weight residual 1.549 1.242 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C11 CHO A 702 " pdb=" C12 CHO A 702 " ideal model delta sigma weight residual 1.529 1.812 -0.283 2.00e-02 2.50e+03 2.00e+02 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 94.96 - 102.76: 39 102.76 - 110.56: 1910 110.56 - 118.36: 3418 118.36 - 126.17: 3785 126.17 - 133.97: 99 Bond angle restraints: 9251 Sorted by residual: angle pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.12e+01 angle pdb=" N MET A 229 " pdb=" CA MET A 229 " pdb=" CB MET A 229 " ideal model delta sigma weight residual 110.42 104.69 5.73 1.18e+00 7.18e-01 2.36e+01 angle pdb=" CA GLU H 46 " pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " ideal model delta sigma weight residual 112.70 126.25 -13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" CA LYS A 151 " pdb=" C LYS A 151 " pdb=" O LYS A 151 " ideal model delta sigma weight residual 120.90 116.14 4.76 1.07e+00 8.73e-01 1.98e+01 ... (remaining 9246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 3935 25.81 - 51.63: 255 51.63 - 77.44: 39 77.44 - 103.25: 7 103.25 - 129.07: 12 Dihedral angle restraints: 4248 sinusoidal: 1782 harmonic: 2466 Sorted by residual: dihedral pdb=" CA TYR A 183 " pdb=" C TYR A 183 " pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C5 CHO A 703 " pdb=" C6 CHO A 703 " pdb=" C7 CHO A 703 " pdb=" O7 CHO A 703 " ideal model delta sinusoidal sigma weight residual 287.57 158.50 129.07 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C5 CHO A 702 " pdb=" C6 CHO A 702 " pdb=" C7 CHO A 702 " pdb=" O7 CHO A 702 " ideal model delta sinusoidal sigma weight residual 287.57 163.57 124.00 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 1065 0.331 - 0.662: 3 0.662 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.654: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C13 CHO A 702 " pdb=" C12 CHO A 702 " pdb=" C14 CHO A 702 " pdb=" C17 CHO A 702 " both_signs ideal model delta sigma weight residual False -2.94 -1.29 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C13 CHO A 703 " pdb=" C12 CHO A 703 " pdb=" C14 CHO A 703 " pdb=" C17 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.94 -1.30 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C9 CHO A 703 " pdb=" C10 CHO A 703 " pdb=" C11 CHO A 703 " pdb=" C8 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.52 -2.05 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 1067 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS L 107 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS L 107 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG L 108 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 57 " 0.059 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 58 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 150 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU A 150 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 150 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 151 " 0.015 2.00e-02 2.50e+03 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 6147 3.25 - 3.80: 10105 3.80 - 4.35: 13056 4.35 - 4.90: 22655 Nonbonded interactions: 52105 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb=" OG SER K 100A" model vdw 2.152 2.440 nonbonded pdb=" OG SER L 182 " pdb=" OD2 ASP L 185 " model vdw 2.210 2.440 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.285 2.440 nonbonded pdb=" OG SER K 17 " pdb=" OD1 ASN K 82A" model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG L 66 " pdb=" O GLY L 68 " model vdw 2.324 2.520 ... (remaining 52100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.48 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.400 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.760 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.013 0.331 6799 Z= 0.752 Angle : 0.754 13.548 9251 Z= 0.364 Chirality : 0.087 1.654 1070 Planarity : 0.005 0.084 1133 Dihedral : 18.278 129.069 2667 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.69 % Allowed : 14.42 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.17 (0.29), residues: 846 helix: 1.90 (0.33), residues: 260 sheet: 1.43 (0.35), residues: 211 loop : -0.41 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 93 HIS 0.024 0.003 HIS H 200 PHE 0.006 0.001 PHE A 37 TYR 0.024 0.001 TYR L 140 ARG 0.005 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 108 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7020 (ptm-80) REVERT: L 142 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7071 (ttt-90) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 1.1430 time to fit residues: 113.5522 Evaluate side-chains 91 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 76 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN H 100EGLN H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6799 Z= 0.220 Angle : 0.595 7.900 9251 Z= 0.294 Chirality : 0.045 0.282 1070 Planarity : 0.005 0.037 1133 Dihedral : 8.675 59.987 1206 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.57 % Allowed : 14.01 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.05 (0.29), residues: 846 helix: 1.71 (0.32), residues: 261 sheet: 1.46 (0.34), residues: 221 loop : -0.54 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE A 128 TYR 0.011 0.001 TYR A 238 ARG 0.002 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8640 (mmm) cc_final: 0.8223 (mmm) REVERT: L 82 ASP cc_start: 0.9016 (m-30) cc_final: 0.8733 (m-30) REVERT: L 108 ARG cc_start: 0.7518 (ttp80) cc_final: 0.6829 (ptm-80) outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 1.0938 time to fit residues: 120.3092 Evaluate side-chains 101 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 55 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6799 Z= 0.163 Angle : 0.522 6.383 9251 Z= 0.262 Chirality : 0.042 0.250 1070 Planarity : 0.004 0.036 1133 Dihedral : 7.447 56.363 1200 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.30 % Allowed : 15.93 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.12 (0.29), residues: 846 helix: 1.76 (0.33), residues: 260 sheet: 1.60 (0.34), residues: 219 loop : -0.55 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 100H HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE A 37 TYR 0.010 0.001 TYR A 238 ARG 0.001 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8665 (mmm) cc_final: 0.8343 (mmm) REVERT: L 82 ASP cc_start: 0.9013 (m-30) cc_final: 0.8735 (m-30) REVERT: L 105 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: L 108 ARG cc_start: 0.7440 (ttp80) cc_final: 0.6680 (ptm-80) REVERT: L 142 ARG cc_start: 0.7233 (tmt90) cc_final: 0.6877 (ttt-90) outliers start: 23 outliers final: 12 residues processed: 101 average time/residue: 1.1084 time to fit residues: 118.5062 Evaluate side-chains 100 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN H 100EGLN H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6799 Z= 0.152 Angle : 0.505 7.257 9251 Z= 0.253 Chirality : 0.041 0.242 1070 Planarity : 0.004 0.036 1133 Dihedral : 6.892 53.994 1196 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.98 % Allowed : 16.48 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.13 (0.29), residues: 846 helix: 1.78 (0.33), residues: 260 sheet: 1.65 (0.35), residues: 219 loop : -0.58 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.001 0.000 HIS A 54 PHE 0.007 0.001 PHE A 37 TYR 0.009 0.001 TYR A 238 ARG 0.001 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8677 (mmm) cc_final: 0.8298 (mmm) REVERT: L 82 ASP cc_start: 0.9007 (m-30) cc_final: 0.8734 (m-30) REVERT: L 105 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: L 108 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6626 (ptm-80) REVERT: L 142 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6733 (ttt-90) outliers start: 28 outliers final: 15 residues processed: 103 average time/residue: 0.9971 time to fit residues: 109.2400 Evaluate side-chains 102 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.0060 chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.0000 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 293 GLN H 100EGLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6799 Z= 0.143 Angle : 0.489 6.135 9251 Z= 0.246 Chirality : 0.041 0.238 1070 Planarity : 0.004 0.036 1133 Dihedral : 6.645 52.652 1196 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.57 % Allowed : 17.31 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.19 (0.29), residues: 846 helix: 1.83 (0.33), residues: 260 sheet: 1.71 (0.34), residues: 219 loop : -0.58 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.000 HIS A 54 PHE 0.007 0.001 PHE A 37 TYR 0.009 0.001 TYR A 238 ARG 0.001 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8685 (mmm) cc_final: 0.8232 (mmm) REVERT: H 99 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6960 (mm-40) REVERT: H 105 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7015 (pp30) REVERT: L 108 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6557 (ptm-80) REVERT: L 142 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6904 (ttt-90) outliers start: 25 outliers final: 13 residues processed: 100 average time/residue: 1.0274 time to fit residues: 109.2125 Evaluate side-chains 100 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 0.0060 chunk 26 optimal weight: 0.0970 chunk 42 optimal weight: 10.0000 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100EGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6799 Z= 0.124 Angle : 0.472 7.047 9251 Z= 0.236 Chirality : 0.040 0.233 1070 Planarity : 0.004 0.036 1133 Dihedral : 6.185 50.550 1196 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.43 % Allowed : 17.03 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.31 (0.29), residues: 846 helix: 1.97 (0.33), residues: 260 sheet: 1.83 (0.34), residues: 218 loop : -0.57 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.001 0.000 HIS L 189 PHE 0.006 0.001 PHE L 139 TYR 0.008 0.001 TYR A 238 ARG 0.001 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8659 (mmm) cc_final: 0.8166 (mmm) REVERT: A 193 ILE cc_start: 0.7846 (tp) cc_final: 0.7430 (mp) REVERT: A 215 MET cc_start: 0.7932 (mmm) cc_final: 0.7436 (mmp) REVERT: H 99 GLN cc_start: 0.7219 (mm-40) cc_final: 0.7012 (mm110) REVERT: H 100 GLN cc_start: 0.5489 (pm20) cc_final: 0.5257 (pm20) REVERT: L 11 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8161 (tt) REVERT: L 105 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: L 108 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6408 (ptm-80) REVERT: L 142 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6853 (ttt-90) outliers start: 24 outliers final: 11 residues processed: 103 average time/residue: 0.8592 time to fit residues: 93.7126 Evaluate side-chains 100 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6799 Z= 0.308 Angle : 0.589 6.595 9251 Z= 0.297 Chirality : 0.044 0.238 1070 Planarity : 0.005 0.043 1133 Dihedral : 6.971 54.310 1196 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.98 % Allowed : 17.45 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.00 (0.29), residues: 846 helix: 1.65 (0.33), residues: 260 sheet: 1.72 (0.34), residues: 218 loop : -0.75 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 100C HIS 0.003 0.001 HIS H 164 PHE 0.029 0.002 PHE K 67 TYR 0.018 0.002 TYR H 100D ARG 0.003 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8709 (mmm) cc_final: 0.8223 (mmm) REVERT: L 79 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7591 (mp10) REVERT: L 82 ASP cc_start: 0.9059 (m-30) cc_final: 0.8750 (m-30) REVERT: L 105 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: L 108 ARG cc_start: 0.7414 (ttp80) cc_final: 0.6754 (ptm-80) REVERT: L 142 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6771 (ttt-90) outliers start: 28 outliers final: 18 residues processed: 109 average time/residue: 1.0709 time to fit residues: 123.9550 Evaluate side-chains 107 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100EGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6799 Z= 0.221 Angle : 0.531 6.381 9251 Z= 0.270 Chirality : 0.042 0.237 1070 Planarity : 0.005 0.036 1133 Dihedral : 6.721 52.503 1196 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.98 % Allowed : 18.27 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.96 (0.29), residues: 846 helix: 1.71 (0.33), residues: 260 sheet: 1.62 (0.35), residues: 214 loop : -0.77 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.000 HIS L 189 PHE 0.017 0.001 PHE K 67 TYR 0.014 0.001 TYR A 238 ARG 0.002 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8660 (mmm) cc_final: 0.8181 (mmm) REVERT: L 79 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7614 (mp10) REVERT: L 82 ASP cc_start: 0.9070 (m-30) cc_final: 0.8757 (m-30) REVERT: L 105 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7074 (pt0) REVERT: L 108 ARG cc_start: 0.7348 (ttp80) cc_final: 0.6682 (ptm-80) REVERT: L 142 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6830 (ttt-90) outliers start: 28 outliers final: 21 residues processed: 104 average time/residue: 1.0471 time to fit residues: 115.4801 Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN H 100EGLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6799 Z= 0.249 Angle : 0.554 6.443 9251 Z= 0.280 Chirality : 0.042 0.235 1070 Planarity : 0.005 0.036 1133 Dihedral : 6.848 54.455 1196 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.98 % Allowed : 18.54 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.85 (0.29), residues: 846 helix: 1.62 (0.33), residues: 260 sheet: 1.59 (0.35), residues: 214 loop : -0.85 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 100H HIS 0.002 0.001 HIS H 164 PHE 0.016 0.002 PHE K 67 TYR 0.016 0.001 TYR H 100D ARG 0.002 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8656 (mmm) cc_final: 0.8193 (mmm) REVERT: L 79 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7644 (mp10) REVERT: L 82 ASP cc_start: 0.9080 (m-30) cc_final: 0.8750 (m-30) REVERT: L 105 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: L 108 ARG cc_start: 0.7373 (ttp80) cc_final: 0.6712 (ptm-80) REVERT: L 142 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6842 (ttt-90) outliers start: 28 outliers final: 20 residues processed: 104 average time/residue: 1.0308 time to fit residues: 113.8095 Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 0.0000 chunk 51 optimal weight: 0.0050 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100EGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6799 Z= 0.125 Angle : 0.481 6.082 9251 Z= 0.245 Chirality : 0.040 0.232 1070 Planarity : 0.004 0.036 1133 Dihedral : 6.247 50.834 1196 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 20.47 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.10 (0.29), residues: 846 helix: 1.86 (0.33), residues: 260 sheet: 1.71 (0.35), residues: 214 loop : -0.71 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.001 0.000 HIS L 189 PHE 0.011 0.001 PHE K 67 TYR 0.014 0.001 TYR A 238 ARG 0.004 0.000 ARG H 100F ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8608 (mmm) cc_final: 0.8148 (mmm) REVERT: A 215 MET cc_start: 0.7937 (mmm) cc_final: 0.7472 (mmp) REVERT: A 279 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7778 (mm) REVERT: L 79 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7617 (mp10) REVERT: L 82 ASP cc_start: 0.9053 (m-30) cc_final: 0.8751 (m-30) REVERT: L 108 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6480 (ptm-80) REVERT: L 142 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6924 (ttt-90) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 1.0962 time to fit residues: 118.3063 Evaluate side-chains 101 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100EGLN H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.191935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136397 restraints weight = 22365.100| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 5.58 r_work: 0.3074 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6799 Z= 0.129 Angle : 0.482 7.755 9251 Z= 0.241 Chirality : 0.040 0.227 1070 Planarity : 0.004 0.036 1133 Dihedral : 5.931 52.926 1196 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.79 % Allowed : 21.02 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 846 helix: 1.75 (0.33), residues: 266 sheet: 1.79 (0.35), residues: 214 loop : -0.65 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.001 0.000 HIS L 189 PHE 0.009 0.001 PHE K 67 TYR 0.012 0.001 TYR A 238 ARG 0.001 0.000 ARG H 100F Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.48 seconds wall clock time: 51 minutes 55.23 seconds (3115.23 seconds total)