Starting phenix.real_space_refine on Thu Jul 18 23:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/07_2024/8wy0_37914.cif" } resolution = 3.8 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= 0.002 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 37 5.16 5 C 3021 2.51 5 N 738 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 27": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.29, per 1000 atoms: 0.71 Number of scatterers: 4656 At special positions: 0 Unit cell: (70.0245, 90.4932, 106.653, 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 37 16.00 O 860 8.00 N 738 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.18 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " 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: 1.78 Conformation dependent library (CDL) restraints added in 815.8 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 39.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'a' and resid 27 through 52 removed outlier: 3.961A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 56 Processing helix chain 'd' and resid 102 through 126 removed outlier: 3.620A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 152 removed outlier: 3.754A pdb=" N THR e 132 " --> pdb=" O MET e 128 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER e 152 " --> pdb=" O VAL e 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.773A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.552A pdb=" N VAL f 130 " --> pdb=" O ASP f 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS f 153 " --> pdb=" O TYR f 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.513A pdb=" N LYS g 79 " --> pdb=" O SER g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 135 Processing helix chain 'm' and resid 260 through 291 removed outlier: 3.528A pdb=" N LEU m 266 " --> pdb=" O ASN m 262 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU m 269 " --> pdb=" O SER m 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA m 280 " --> pdb=" O ALA m 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA m 291 " --> pdb=" O ALA m 287 " (cutoff:3.500A) Processing helix chain 'n' and resid 272 through 307 removed outlier: 3.927A pdb=" N TYR n 283 " --> pdb=" O THR n 279 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET n 284 " --> pdb=" O SER n 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 7.349A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.817A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.506A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.985A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 114 removed outlier: 5.541A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.632A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 33 removed outlier: 3.910A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 55 through 57 removed outlier: 3.705A pdb=" N GLN g 86 " --> pdb=" O PHE g 56 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 615 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: 1.09 Time building geometry restraints manager: 1.95 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: 1440 1.34 - 1.46: 1109 1.46 - 1.59: 2143 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4743 Sorted by residual: bond pdb=" CA THR f 34 " pdb=" CB THR f 34 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.68e-02 3.54e+03 2.19e+00 bond pdb=" CA LEU g 110 " pdb=" CB LEU g 110 " ideal model delta sigma weight residual 1.528 1.564 -0.035 2.61e-02 1.47e+03 1.83e+00 bond pdb=" CA ASN e 121 " pdb=" CB ASN e 121 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.37e-02 5.33e+03 1.18e+00 bond pdb=" C3 CLR b 201 " pdb=" O1 CLR b 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB ASN d 36 " pdb=" CG ASN d 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 ... (remaining 4738 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 132 107.39 - 114.04: 2712 114.04 - 120.69: 1900 120.69 - 127.35: 1655 127.35 - 134.00: 31 Bond angle restraints: 6430 Sorted by residual: angle pdb=" CA LYS d 80 " pdb=" CB LYS d 80 " pdb=" CG LYS d 80 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA TYR d 79 " pdb=" CB TYR d 79 " pdb=" CG TYR d 79 " ideal model delta sigma weight residual 113.90 119.74 -5.84 1.80e+00 3.09e-01 1.05e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" C PRO g 96 " ideal model delta sigma weight residual 110.40 115.33 -4.93 1.61e+00 3.86e-01 9.38e+00 angle pdb=" CB LYS f 85 " pdb=" CG LYS f 85 " pdb=" CD LYS f 85 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.96e+00 angle pdb=" CB MET g 103 " pdb=" CG MET g 103 " pdb=" SD MET g 103 " ideal model delta sigma weight residual 112.70 120.71 -8.01 3.00e+00 1.11e-01 7.12e+00 ... (remaining 6425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2413 17.75 - 35.50: 374 35.50 - 53.25: 95 53.25 - 70.99: 10 70.99 - 88.74: 5 Dihedral angle restraints: 2897 sinusoidal: 1190 harmonic: 1707 Sorted by residual: dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual 93.00 145.92 -52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CA ASN g 106 " pdb=" C ASN g 106 " pdb=" N CYS g 107 " pdb=" CA CYS g 107 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 53.21 39.79 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 2894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 603 0.047 - 0.095: 123 0.095 - 0.142: 32 0.142 - 0.189: 0 0.189 - 0.237: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CB ILE f 133 " pdb=" CA ILE f 133 " pdb=" CG1 ILE f 133 " pdb=" CG2 ILE f 133 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA GLU f 91 " pdb=" N GLU f 91 " pdb=" C GLU f 91 " pdb=" CB GLU f 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE d 24 " pdb=" N ILE d 24 " pdb=" C ILE d 24 " pdb=" CB ILE d 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 756 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN e 121 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN e 121 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN e 121 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS e 122 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU g 97 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU g 97 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU g 97 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN g 98 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO g 96 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " -0.021 5.00e-02 4.00e+02 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 152 2.69 - 3.25: 4671 3.25 - 3.80: 7081 3.80 - 4.35: 8584 4.35 - 4.90: 14176 Nonbonded interactions: 34664 Sorted by model distance: nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.142 2.440 nonbonded pdb=" OG SER f 88 " pdb=" OE1 GLU f 91 " model vdw 2.155 2.440 nonbonded pdb=" O ASN e 121 " pdb=" ND2 ASN e 121 " model vdw 2.166 2.520 nonbonded pdb=" OD1 ASP e 126 " pdb=" OG SER e 129 " model vdw 2.186 2.440 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.204 2.440 ... (remaining 34659 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' and resid 27 through 54) selection = (chain 'b' and resid 27 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 : 0.003 0.035 4743 Z= 0.201 Angle : 0.710 8.769 6430 Z= 0.363 Chirality : 0.041 0.237 759 Planarity : 0.004 0.038 786 Dihedral : 17.421 88.742 1776 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.16 % Allowed : 36.87 % Favored : 61.97 % 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: -1.58 (0.34), residues: 569 helix: 1.39 (0.35), residues: 215 sheet: -2.08 (0.55), residues: 84 loop : -2.88 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 PHE 0.012 0.001 PHE n 296 TYR 0.025 0.002 TYR f 99 ARG 0.005 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 47 THR cc_start: 0.8423 (m) cc_final: 0.8167 (p) REVERT: b 52 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6358 (ttm170) REVERT: d 27 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8242 (mt-10) REVERT: d 43 TRP cc_start: 0.7895 (t60) cc_final: 0.7634 (t60) REVERT: e 72 ASP cc_start: 0.7079 (m-30) cc_final: 0.6803 (m-30) REVERT: e 74 ASN cc_start: 0.8062 (m-40) cc_final: 0.7771 (m110) REVERT: f 37 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6564 (tptp) REVERT: f 60 GLN cc_start: 0.7220 (pm20) cc_final: 0.6861 (mt0) REVERT: f 117 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7824 (ttp-110) REVERT: f 123 MET cc_start: 0.6624 (ttt) cc_final: 0.6176 (ttm) REVERT: g 71 LYS cc_start: 0.6165 (mtmt) cc_final: 0.5918 (mttt) REVERT: m 288 LYS cc_start: 0.7961 (tptt) cc_final: 0.7590 (tmtt) REVERT: n 275 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7928 (tm-30) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.1687 time to fit residues: 40.3066 Evaluate side-chains 177 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.0570 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4743 Z= 0.207 Angle : 0.652 7.914 6430 Z= 0.326 Chirality : 0.042 0.170 759 Planarity : 0.004 0.040 786 Dihedral : 5.378 48.804 701 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 7.92 % Allowed : 29.73 % Favored : 62.36 % 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: -1.02 (0.35), residues: 569 helix: 2.14 (0.34), residues: 217 sheet: -2.05 (0.54), residues: 86 loop : -2.77 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP f 59 HIS 0.005 0.001 HIS f 81 PHE 0.014 0.002 PHE n 296 TYR 0.029 0.002 TYR f 99 ARG 0.003 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7190 (tpt170) cc_final: 0.6620 (ttm170) REVERT: d 22 PHE cc_start: 0.5050 (m-80) cc_final: 0.3954 (m-80) REVERT: d 27 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7738 (tt0) REVERT: d 34 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: d 79 TYR cc_start: 0.8124 (t80) cc_final: 0.7918 (t80) REVERT: e 40 ILE cc_start: 0.8536 (mt) cc_final: 0.8301 (mt) REVERT: e 72 ASP cc_start: 0.7051 (m-30) cc_final: 0.6785 (m-30) REVERT: e 74 ASN cc_start: 0.7999 (m-40) cc_final: 0.7741 (m110) REVERT: f 37 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6916 (tptt) REVERT: f 79 GLU cc_start: 0.3387 (OUTLIER) cc_final: 0.2379 (mm-30) REVERT: f 92 GLN cc_start: 0.6864 (mt0) cc_final: 0.6661 (mt0) REVERT: f 106 GLU cc_start: 0.8561 (pm20) cc_final: 0.8273 (pm20) REVERT: g 71 LYS cc_start: 0.6307 (mtmt) cc_final: 0.5971 (mmtm) REVERT: m 288 LYS cc_start: 0.8015 (tptt) cc_final: 0.7679 (tmtt) REVERT: n 275 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8000 (tm-30) outliers start: 41 outliers final: 25 residues processed: 190 average time/residue: 0.1638 time to fit residues: 38.7301 Evaluate side-chains 194 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4743 Z= 0.200 Angle : 0.632 7.939 6430 Z= 0.316 Chirality : 0.041 0.141 759 Planarity : 0.004 0.037 786 Dihedral : 5.233 47.832 699 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 7.53 % Allowed : 32.82 % Favored : 59.65 % 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: -0.81 (0.36), residues: 569 helix: 2.36 (0.34), residues: 217 sheet: -2.10 (0.53), residues: 96 loop : -2.62 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.011 0.001 PHE n 296 TYR 0.027 0.002 TYR b 33 ARG 0.002 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6856 (ttm170) REVERT: d 22 PHE cc_start: 0.5480 (m-80) cc_final: 0.4005 (m-80) REVERT: d 90 TYR cc_start: 0.8119 (m-80) cc_final: 0.7890 (m-80) REVERT: e 72 ASP cc_start: 0.7135 (m-30) cc_final: 0.6828 (m-30) REVERT: e 74 ASN cc_start: 0.8008 (m-40) cc_final: 0.7723 (m110) REVERT: e 91 GLU cc_start: 0.7959 (tp30) cc_final: 0.7713 (tp30) REVERT: f 37 LYS cc_start: 0.7374 (ttpp) cc_final: 0.6949 (tptt) REVERT: f 92 GLN cc_start: 0.6950 (mt0) cc_final: 0.6713 (mt0) REVERT: f 106 GLU cc_start: 0.8495 (pm20) cc_final: 0.8244 (pm20) REVERT: g 71 LYS cc_start: 0.6273 (mtmt) cc_final: 0.5990 (mmtm) REVERT: m 288 LYS cc_start: 0.7937 (tptt) cc_final: 0.7585 (tmtt) REVERT: m 289 LEU cc_start: 0.7892 (tp) cc_final: 0.7478 (tp) outliers start: 39 outliers final: 30 residues processed: 184 average time/residue: 0.1572 time to fit residues: 36.1283 Evaluate side-chains 189 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.196 Angle : 0.620 7.584 6430 Z= 0.305 Chirality : 0.041 0.132 759 Planarity : 0.004 0.037 786 Dihedral : 5.141 44.371 699 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 9.27 % Allowed : 31.66 % Favored : 59.07 % 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: -0.77 (0.36), residues: 569 helix: 2.42 (0.34), residues: 217 sheet: -2.13 (0.51), residues: 98 loop : -2.60 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.010 0.001 PHE n 296 TYR 0.014 0.001 TYR e 150 ARG 0.002 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6772 (tpp-160) REVERT: d 22 PHE cc_start: 0.4810 (m-80) cc_final: 0.3877 (m-80) REVERT: d 98 GLU cc_start: 0.8188 (tt0) cc_final: 0.7588 (tm-30) REVERT: e 69 ASP cc_start: 0.5470 (OUTLIER) cc_final: 0.5228 (p0) REVERT: e 72 ASP cc_start: 0.7199 (m-30) cc_final: 0.6875 (m-30) REVERT: e 74 ASN cc_start: 0.8036 (m-40) cc_final: 0.7747 (m110) REVERT: f 37 LYS cc_start: 0.7380 (ttpp) cc_final: 0.6980 (tptt) REVERT: f 81 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6695 (t70) REVERT: f 85 LYS cc_start: 0.8068 (tppt) cc_final: 0.7696 (mmmt) REVERT: f 92 GLN cc_start: 0.7006 (mt0) cc_final: 0.6681 (mt0) REVERT: f 104 LYS cc_start: 0.8553 (tptt) cc_final: 0.8271 (mmtm) REVERT: f 125 MET cc_start: 0.8072 (mtp) cc_final: 0.7852 (mtt) REVERT: m 289 LEU cc_start: 0.7877 (tp) cc_final: 0.7447 (tp) outliers start: 48 outliers final: 35 residues processed: 195 average time/residue: 0.1573 time to fit residues: 38.6142 Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 279 THR Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.191 Angle : 0.657 7.206 6430 Z= 0.320 Chirality : 0.041 0.133 759 Planarity : 0.003 0.035 786 Dihedral : 4.829 27.587 697 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 8.49 % Allowed : 32.43 % Favored : 59.07 % 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: -0.77 (0.35), residues: 569 helix: 2.36 (0.34), residues: 217 sheet: -1.90 (0.52), residues: 98 loop : -2.65 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.018 0.002 PHE e 110 TYR 0.025 0.002 TYR b 33 ARG 0.002 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7323 (tpt170) cc_final: 0.6789 (tpp-160) REVERT: d 22 PHE cc_start: 0.4587 (m-80) cc_final: 0.3876 (m-80) REVERT: d 98 GLU cc_start: 0.8163 (tt0) cc_final: 0.7572 (tm-30) REVERT: e 69 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.5223 (p0) REVERT: e 72 ASP cc_start: 0.7227 (m-30) cc_final: 0.6894 (m-30) REVERT: e 74 ASN cc_start: 0.8020 (m-40) cc_final: 0.7725 (m110) REVERT: e 101 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8462 (ptp90) REVERT: f 37 LYS cc_start: 0.7347 (ttpp) cc_final: 0.6975 (tptp) REVERT: f 81 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6684 (t70) REVERT: f 92 GLN cc_start: 0.7145 (mt0) cc_final: 0.6805 (mt0) REVERT: f 125 MET cc_start: 0.8012 (mtp) cc_final: 0.7780 (mtt) REVERT: m 289 LEU cc_start: 0.7933 (tp) cc_final: 0.7467 (tp) outliers start: 44 outliers final: 38 residues processed: 184 average time/residue: 0.1452 time to fit residues: 34.1631 Evaluate side-chains 197 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.173 Angle : 0.661 7.235 6430 Z= 0.319 Chirality : 0.042 0.175 759 Planarity : 0.003 0.034 786 Dihedral : 4.761 29.282 697 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 8.11 % Allowed : 34.36 % Favored : 57.53 % 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: -0.69 (0.35), residues: 569 helix: 2.40 (0.34), residues: 217 sheet: -1.79 (0.51), residues: 100 loop : -2.61 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.015 0.001 PHE e 110 TYR 0.022 0.001 TYR b 33 ARG 0.002 0.000 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.4585 (m-80) cc_final: 0.3948 (m-80) REVERT: d 57 ARG cc_start: 0.8177 (ttt90) cc_final: 0.7967 (ttt90) REVERT: e 69 ASP cc_start: 0.5470 (OUTLIER) cc_final: 0.5232 (p0) REVERT: e 72 ASP cc_start: 0.7256 (m-30) cc_final: 0.6924 (m-30) REVERT: e 101 ARG cc_start: 0.8794 (ptp90) cc_final: 0.8440 (ptp90) REVERT: f 37 LYS cc_start: 0.7536 (ttpp) cc_final: 0.7327 (tptp) REVERT: f 85 LYS cc_start: 0.8051 (tppt) cc_final: 0.7769 (mmmt) REVERT: f 92 GLN cc_start: 0.7145 (mt0) cc_final: 0.6722 (mt0) REVERT: f 125 MET cc_start: 0.7956 (mtp) cc_final: 0.7734 (mtt) REVERT: g 85 TYR cc_start: 0.7963 (m-80) cc_final: 0.7702 (m-80) REVERT: m 289 LEU cc_start: 0.7961 (tp) cc_final: 0.7525 (tp) outliers start: 42 outliers final: 35 residues processed: 187 average time/residue: 0.1522 time to fit residues: 36.0679 Evaluate side-chains 197 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain n residue 279 THR Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 74 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4743 Z= 0.248 Angle : 0.731 8.437 6430 Z= 0.357 Chirality : 0.043 0.176 759 Planarity : 0.004 0.035 786 Dihedral : 4.980 24.723 697 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 9.85 % Allowed : 33.59 % Favored : 56.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.35), residues: 569 helix: 2.32 (0.34), residues: 217 sheet: -1.64 (0.53), residues: 97 loop : -2.56 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.010 0.002 PHE b 40 TYR 0.017 0.002 TYR e 150 ARG 0.012 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.4673 (m-80) cc_final: 0.4278 (m-80) REVERT: d 79 TYR cc_start: 0.7828 (t80) cc_final: 0.7582 (t80) REVERT: e 69 ASP cc_start: 0.5415 (OUTLIER) cc_final: 0.5141 (p0) REVERT: e 72 ASP cc_start: 0.7332 (m-30) cc_final: 0.6947 (m-30) REVERT: e 101 ARG cc_start: 0.8824 (ptp90) cc_final: 0.8510 (ptp90) REVERT: e 119 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7668 (p) REVERT: f 37 LYS cc_start: 0.7536 (ttpp) cc_final: 0.7276 (tptp) REVERT: f 85 LYS cc_start: 0.8225 (tppt) cc_final: 0.7899 (mmmt) REVERT: f 92 GLN cc_start: 0.7396 (mt0) cc_final: 0.6984 (mt0) REVERT: f 125 MET cc_start: 0.7946 (mtp) cc_final: 0.7744 (mtt) REVERT: m 264 MET cc_start: 0.7728 (tpp) cc_final: 0.7482 (tpp) REVERT: m 289 LEU cc_start: 0.7951 (tp) cc_final: 0.7526 (tp) outliers start: 51 outliers final: 40 residues processed: 188 average time/residue: 0.1521 time to fit residues: 36.4043 Evaluate side-chains 200 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 279 THR Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.203 Angle : 0.724 8.779 6430 Z= 0.347 Chirality : 0.042 0.147 759 Planarity : 0.004 0.035 786 Dihedral : 5.017 32.760 697 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 7.72 % Allowed : 35.14 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.35), residues: 569 helix: 2.27 (0.34), residues: 217 sheet: -1.59 (0.53), residues: 95 loop : -2.48 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.009 0.001 PHE n 296 TYR 0.025 0.002 TYR f 99 ARG 0.010 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8163 (t80) cc_final: 0.7854 (t80) REVERT: b 52 ARG cc_start: 0.7969 (ttp80) cc_final: 0.6498 (ttm170) REVERT: d 22 PHE cc_start: 0.4714 (m-80) cc_final: 0.4000 (m-80) REVERT: e 69 ASP cc_start: 0.5496 (OUTLIER) cc_final: 0.5226 (p0) REVERT: e 72 ASP cc_start: 0.7330 (m-30) cc_final: 0.6940 (m-30) REVERT: e 101 ARG cc_start: 0.8809 (ptp90) cc_final: 0.8544 (ptp90) REVERT: e 109 ASN cc_start: 0.7625 (m-40) cc_final: 0.7180 (p0) REVERT: e 117 ARG cc_start: 0.7603 (ttt-90) cc_final: 0.7099 (ttt-90) REVERT: e 119 CYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7663 (p) REVERT: f 37 LYS cc_start: 0.7559 (ttpp) cc_final: 0.7334 (tptp) REVERT: f 85 LYS cc_start: 0.8086 (tppt) cc_final: 0.7772 (mmmt) REVERT: f 92 GLN cc_start: 0.7456 (mt0) cc_final: 0.7032 (mt0) REVERT: f 111 TYR cc_start: 0.7447 (m-80) cc_final: 0.6410 (m-80) REVERT: m 264 MET cc_start: 0.7558 (tpp) cc_final: 0.7259 (tpp) REVERT: m 289 LEU cc_start: 0.8013 (tp) cc_final: 0.7571 (tp) outliers start: 40 outliers final: 35 residues processed: 187 average time/residue: 0.1615 time to fit residues: 37.8789 Evaluate side-chains 201 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4743 Z= 0.199 Angle : 0.732 8.781 6430 Z= 0.351 Chirality : 0.042 0.138 759 Planarity : 0.003 0.033 786 Dihedral : 5.016 32.292 697 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.72 % Allowed : 36.29 % Favored : 55.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.62 (0.35), residues: 569 helix: 2.32 (0.34), residues: 217 sheet: -1.60 (0.52), residues: 93 loop : -2.49 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.009 0.001 PHE g 135 TYR 0.020 0.001 TYR n 283 ARG 0.008 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8098 (t80) cc_final: 0.7851 (t80) REVERT: b 55 PHE cc_start: 0.6968 (t80) cc_final: 0.6760 (m-80) REVERT: d 57 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7779 (ttt90) REVERT: e 69 ASP cc_start: 0.5395 (OUTLIER) cc_final: 0.5111 (p0) REVERT: e 72 ASP cc_start: 0.7332 (m-30) cc_final: 0.6942 (m-30) REVERT: e 101 ARG cc_start: 0.8787 (ptp90) cc_final: 0.8517 (ptp90) REVERT: e 109 ASN cc_start: 0.7650 (m-40) cc_final: 0.7208 (p0) REVERT: e 117 ARG cc_start: 0.7593 (ttt-90) cc_final: 0.7162 (ttt-90) REVERT: e 119 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7648 (p) REVERT: f 37 LYS cc_start: 0.7504 (ttpp) cc_final: 0.7297 (tptp) REVERT: f 92 GLN cc_start: 0.7356 (mt0) cc_final: 0.6963 (mt0) REVERT: f 106 GLU cc_start: 0.8555 (pm20) cc_final: 0.8308 (pm20) REVERT: f 111 TYR cc_start: 0.7451 (m-80) cc_final: 0.6438 (m-80) REVERT: m 289 LEU cc_start: 0.7958 (tp) cc_final: 0.7517 (tp) outliers start: 40 outliers final: 33 residues processed: 188 average time/residue: 0.1622 time to fit residues: 38.2606 Evaluate side-chains 199 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4743 Z= 0.211 Angle : 0.745 8.954 6430 Z= 0.359 Chirality : 0.042 0.144 759 Planarity : 0.004 0.034 786 Dihedral : 4.981 31.330 697 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.95 % Allowed : 36.87 % Favored : 56.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.65 (0.35), residues: 569 helix: 2.26 (0.34), residues: 217 sheet: -1.42 (0.55), residues: 86 loop : -2.55 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.012 0.001 PHE f 87 TYR 0.024 0.001 TYR n 283 ARG 0.012 0.001 ARG b 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 40 PHE cc_start: 0.8115 (t80) cc_final: 0.7911 (t80) REVERT: b 52 ARG cc_start: 0.8010 (ttp80) cc_final: 0.6340 (ttm170) REVERT: b 55 PHE cc_start: 0.7121 (t80) cc_final: 0.6834 (m-80) REVERT: d 57 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7722 (ttt90) REVERT: e 69 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4910 (p0) REVERT: e 72 ASP cc_start: 0.7283 (m-30) cc_final: 0.6897 (m-30) REVERT: e 101 ARG cc_start: 0.8791 (ptp90) cc_final: 0.8519 (ptp90) REVERT: e 109 ASN cc_start: 0.7863 (m-40) cc_final: 0.7331 (p0) REVERT: e 117 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7176 (ttt-90) REVERT: e 119 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7654 (p) REVERT: f 37 LYS cc_start: 0.7545 (ttpp) cc_final: 0.7275 (tptp) REVERT: f 85 LYS cc_start: 0.8114 (tppt) cc_final: 0.7882 (mmmt) REVERT: f 92 GLN cc_start: 0.7404 (mt0) cc_final: 0.6925 (mt0) REVERT: f 106 GLU cc_start: 0.8530 (pm20) cc_final: 0.8296 (pm20) REVERT: f 111 TYR cc_start: 0.7414 (m-80) cc_final: 0.6377 (m-80) REVERT: m 264 MET cc_start: 0.7527 (tpp) cc_final: 0.7247 (tpp) REVERT: m 289 LEU cc_start: 0.7972 (tp) cc_final: 0.7515 (tp) REVERT: n 275 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7846 (tm-30) outliers start: 36 outliers final: 34 residues processed: 184 average time/residue: 0.1581 time to fit residues: 36.6526 Evaluate side-chains 200 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 263 MET Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 61 HIS ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135798 restraints weight = 7492.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139779 restraints weight = 4211.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142462 restraints weight = 2896.158| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.194 Angle : 0.735 10.291 6430 Z= 0.356 Chirality : 0.042 0.177 759 Planarity : 0.003 0.032 786 Dihedral : 4.878 30.737 697 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.95 % Allowed : 37.84 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.55 (0.35), residues: 569 helix: 2.28 (0.34), residues: 218 sheet: -1.22 (0.56), residues: 86 loop : -2.51 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.024 0.001 PHE e 110 TYR 0.021 0.001 TYR n 283 ARG 0.011 0.001 ARG b 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.87 seconds wall clock time: 26 minutes 45.29 seconds (1605.29 seconds total)