Starting phenix.real_space_refine on Wed Jan 17 23:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/01_2024/7crb_30449.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4318 2.51 5 N 1155 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 117": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 221": "OE1" <-> "OE2" Residue "J GLU 249": "OE1" <-> "OE2" Residue "J GLU 270": "OE1" <-> "OE2" Residue "J ARG 271": "NH1" <-> "NH2" Residue "J GLU 299": "OE1" <-> "OE2" Residue "J GLU 300": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A GLU 965": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A GLU 1133": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A GLU 1167": "OE1" <-> "OE2" 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: 6806 Number of models: 1 Model: "" Number of chains: 2 Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "A" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4926 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 27, 'TRANS': 588} Time building chain proxies: 3.90, per 1000 atoms: 0.57 Number of scatterers: 6806 At special positions: 0 Unit cell: (84.5383, 114.182, 93.3215, 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 39 16.00 O 1294 8.00 N 1155 7.00 C 4318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 31.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'J' and resid 68 through 84 removed outlier: 4.227A pdb=" N SER J 84 " --> pdb=" O HIS J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 102 removed outlier: 4.607A pdb=" N VAL J 95 " --> pdb=" O MET J 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.531A pdb=" N ALA J 129 " --> pdb=" O THR J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 157 through 177 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 198 through 210 removed outlier: 4.319A pdb=" N PHE J 204 " --> pdb=" O THR J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 223 Processing helix chain 'J' and resid 226 through 239 removed outlier: 3.674A pdb=" N GLU J 239 " --> pdb=" O LEU J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 261 Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 302 through 309 removed outlier: 3.877A pdb=" N TYR J 309 " --> pdb=" O TYR J 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.618A pdb=" N SER A 600 " --> pdb=" O THR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.671A pdb=" N LEU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 626' Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.616A pdb=" N GLN A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.919A pdb=" N GLU A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 880 through 886 removed outlier: 3.732A pdb=" N ILE A 883 " --> pdb=" O PRO A 880 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 884 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 953 removed outlier: 3.889A pdb=" N ILE A 950 " --> pdb=" O PRO A 947 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 4.097A pdb=" N LYS A 968 " --> pdb=" O GLU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 removed outlier: 3.609A pdb=" N LEU A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 975' Processing helix chain 'A' and resid 990 through 996 removed outlier: 3.652A pdb=" N LYS A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1064 Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.513A pdb=" N GLY A 585 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 680 through 682 removed outlier: 6.400A pdb=" N LEU A 681 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N MET A 704 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 797 " --> pdb=" O ASN A 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 788 through 789 removed outlier: 3.583A pdb=" N ILE A 789 " --> pdb=" O ALA A 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 843 through 845 removed outlier: 3.530A pdb=" N ILE A 939 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.707A pdb=" N LEU A 980 " --> pdb=" O ARG A1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1012 through 1013 Processing sheet with id=AA7, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 3.653A pdb=" N VAL A1129 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A1130 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1137 " --> pdb=" O ASP A1132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 3.653A pdb=" N VAL A1129 " --> pdb=" O GLU A1176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1164 216 hydrogen bonds defined for protein. 585 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: 1.89 Time building geometry restraints manager: 2.61 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: 1139 1.31 - 1.43: 1761 1.43 - 1.56: 3987 1.56 - 1.68: 0 1.68 - 1.81: 53 Bond restraints: 6940 Sorted by residual: bond pdb=" C PRO A 947 " pdb=" O PRO A 947 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.71e+01 bond pdb=" CA SER J 296 " pdb=" CB SER J 296 " ideal model delta sigma weight residual 1.531 1.467 0.063 1.62e-02 3.81e+03 1.54e+01 bond pdb=" N LEU A1121 " pdb=" CA LEU A1121 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.33e+00 bond pdb=" N LYS A1122 " pdb=" CA LYS A1122 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.31e+00 bond pdb=" N VAL A1113 " pdb=" CA VAL A1113 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.04e+00 ... (remaining 6935 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 162 105.94 - 112.97: 3809 112.97 - 119.99: 2403 119.99 - 127.01: 2950 127.01 - 134.03: 77 Bond angle restraints: 9401 Sorted by residual: angle pdb=" N SER J 294 " pdb=" CA SER J 294 " pdb=" C SER J 294 " ideal model delta sigma weight residual 113.38 102.25 11.13 1.23e+00 6.61e-01 8.19e+01 angle pdb=" C PRO A 947 " pdb=" CA PRO A 947 " pdb=" CB PRO A 947 " ideal model delta sigma weight residual 110.95 103.18 7.77 1.31e+00 5.83e-01 3.52e+01 angle pdb=" N GLU J 300 " pdb=" CA GLU J 300 " pdb=" C GLU J 300 " ideal model delta sigma weight residual 111.14 105.10 6.04 1.08e+00 8.57e-01 3.13e+01 angle pdb=" N LEU J 301 " pdb=" CA LEU J 301 " pdb=" C LEU J 301 " ideal model delta sigma weight residual 112.92 106.21 6.71 1.23e+00 6.61e-01 2.97e+01 angle pdb=" CA PRO J 265 " pdb=" N PRO J 265 " pdb=" CD PRO J 265 " ideal model delta sigma weight residual 112.00 104.54 7.46 1.40e+00 5.10e-01 2.84e+01 ... (remaining 9396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 3817 16.76 - 33.52: 364 33.52 - 50.27: 57 50.27 - 67.03: 15 67.03 - 83.79: 8 Dihedral angle restraints: 4261 sinusoidal: 1737 harmonic: 2524 Sorted by residual: dihedral pdb=" N LEU J 295 " pdb=" C LEU J 295 " pdb=" CA LEU J 295 " pdb=" CB LEU J 295 " ideal model delta harmonic sigma weight residual 122.80 110.43 12.37 0 2.50e+00 1.60e-01 2.45e+01 dihedral pdb=" CA LEU A 753 " pdb=" C LEU A 753 " pdb=" N HIS A 754 " pdb=" CA HIS A 754 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C PRO A 947 " pdb=" N PRO A 947 " pdb=" CA PRO A 947 " pdb=" CB PRO A 947 " ideal model delta harmonic sigma weight residual -120.70 -110.26 -10.44 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 970 0.077 - 0.153: 102 0.153 - 0.230: 10 0.230 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA LEU J 295 " pdb=" N LEU J 295 " pdb=" C LEU J 295 " pdb=" CB LEU J 295 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLN J 297 " pdb=" N GLN J 297 " pdb=" C GLN J 297 " pdb=" CB GLN J 297 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ILE J 298 " pdb=" N ILE J 298 " pdb=" C ILE J 298 " pdb=" CB ILE J 298 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1082 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 98 " 0.021 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP J 98 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP J 98 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP J 98 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 98 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 98 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 298 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C ILE J 298 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE J 298 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU J 299 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 300 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C GLU J 300 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU J 300 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU J 301 " -0.017 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1933 2.81 - 3.33: 6277 3.33 - 3.86: 10539 3.86 - 4.38: 12704 4.38 - 4.90: 21856 Nonbonded interactions: 53309 Sorted by model distance: nonbonded pdb=" O SER A 949 " pdb=" OG SER A 952 " model vdw 2.288 2.440 nonbonded pdb=" NZ LYS A 690 " pdb=" OE2 GLU A 693 " model vdw 2.299 2.520 nonbonded pdb=" O LEU A1060 " pdb=" OG1 THR A1064 " model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG J 151 " pdb=" OE1 GLU J 167 " model vdw 2.337 2.520 nonbonded pdb=" N SER J 294 " pdb=" N LEU J 295 " model vdw 2.352 2.560 ... (remaining 53304 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=0.43 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: 2.740 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: 9.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.790 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6940 Z= 0.349 Angle : 0.809 11.134 9401 Z= 0.491 Chirality : 0.052 0.384 1085 Planarity : 0.004 0.035 1198 Dihedral : 13.844 83.788 2611 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.77 % Allowed : 0.89 % Favored : 98.34 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.29), residues: 845 helix: -0.88 (0.32), residues: 238 sheet: -2.37 (0.42), residues: 162 loop : -1.47 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP J 98 HIS 0.004 0.001 HIS A 913 PHE 0.022 0.002 PHE A 868 TYR 0.009 0.001 TYR J 305 ARG 0.010 0.001 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: J 297 GLN cc_start: 0.8372 (mp10) cc_final: 0.7906 (mp10) REVERT: A 626 ARG cc_start: 0.6789 (tpt90) cc_final: 0.6564 (tpt-90) REVERT: A 984 LYS cc_start: 0.8705 (mptt) cc_final: 0.8495 (mptt) REVERT: A 1011 VAL cc_start: 0.7845 (p) cc_final: 0.7615 (t) outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.1848 time to fit residues: 22.0849 Evaluate side-chains 67 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain A residue 1103 THR Chi-restraints excluded: chain A residue 1117 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 65 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6940 Z= 0.309 Angle : 0.632 9.465 9401 Z= 0.329 Chirality : 0.044 0.150 1085 Planarity : 0.004 0.043 1198 Dihedral : 6.030 59.900 921 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.30 % Allowed : 7.02 % Favored : 90.68 % 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: -1.96 (0.30), residues: 845 helix: -0.32 (0.34), residues: 246 sheet: -2.25 (0.42), residues: 164 loop : -1.43 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 98 HIS 0.003 0.001 HIS A 913 PHE 0.016 0.001 PHE A 868 TYR 0.010 0.001 TYR J 305 ARG 0.004 0.000 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.1734 time to fit residues: 20.4133 Evaluate side-chains 77 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 277 GLN ** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS A1140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6940 Z= 0.302 Angle : 0.615 11.375 9401 Z= 0.317 Chirality : 0.044 0.154 1085 Planarity : 0.003 0.039 1198 Dihedral : 5.337 38.081 917 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.81 % Allowed : 8.56 % Favored : 88.63 % 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: -1.69 (0.30), residues: 845 helix: 0.06 (0.35), residues: 239 sheet: -2.10 (0.43), residues: 158 loop : -1.37 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 254 HIS 0.004 0.001 HIS A 913 PHE 0.019 0.001 PHE J 269 TYR 0.019 0.001 TYR A1119 ARG 0.002 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 939 ILE cc_start: 0.8496 (mm) cc_final: 0.8289 (mm) outliers start: 22 outliers final: 14 residues processed: 81 average time/residue: 0.1827 time to fit residues: 20.6354 Evaluate side-chains 75 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1180 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.0370 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN J 277 GLN ** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6940 Z= 0.191 Angle : 0.556 10.205 9401 Z= 0.284 Chirality : 0.042 0.153 1085 Planarity : 0.003 0.030 1198 Dihedral : 4.685 19.719 915 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.68 % Allowed : 9.83 % Favored : 87.48 % 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: -1.39 (0.31), residues: 845 helix: 0.38 (0.36), residues: 236 sheet: -2.05 (0.44), residues: 158 loop : -1.16 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.019 0.001 PHE J 269 TYR 0.010 0.001 TYR J 305 ARG 0.002 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.865 Fit side-chains REVERT: J 277 GLN cc_start: 0.7819 (pt0) cc_final: 0.7459 (pt0) REVERT: J 291 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7332 (tm-30) REVERT: J 304 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7023 (tp30) REVERT: A 887 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7641 (mtt90) REVERT: A 939 ILE cc_start: 0.8209 (mm) cc_final: 0.7989 (mm) REVERT: A 945 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: A 1140 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7480 (pp30) outliers start: 21 outliers final: 13 residues processed: 90 average time/residue: 0.2122 time to fit residues: 25.4747 Evaluate side-chains 85 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 149 HIS J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6940 Z= 0.226 Angle : 0.567 9.508 9401 Z= 0.290 Chirality : 0.042 0.168 1085 Planarity : 0.003 0.038 1198 Dihedral : 4.667 20.991 915 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.19 % Allowed : 10.47 % Favored : 86.33 % 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: -1.35 (0.31), residues: 845 helix: 0.44 (0.36), residues: 237 sheet: -2.04 (0.44), residues: 159 loop : -1.14 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 254 HIS 0.004 0.001 HIS A 913 PHE 0.019 0.001 PHE J 269 TYR 0.010 0.001 TYR J 305 ARG 0.001 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 69 time to evaluate : 0.862 Fit side-chains REVERT: A 939 ILE cc_start: 0.8265 (mm) cc_final: 0.8038 (mm) REVERT: A 945 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6496 (pm20) outliers start: 25 outliers final: 17 residues processed: 83 average time/residue: 0.2154 time to fit residues: 23.9039 Evaluate side-chains 84 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6940 Z= 0.241 Angle : 0.574 9.480 9401 Z= 0.294 Chirality : 0.043 0.162 1085 Planarity : 0.003 0.039 1198 Dihedral : 4.697 20.897 915 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.58 % Allowed : 11.24 % Favored : 85.19 % 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: -1.34 (0.31), residues: 845 helix: 0.47 (0.36), residues: 236 sheet: -2.08 (0.43), residues: 159 loop : -1.12 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.019 0.001 PHE J 269 TYR 0.014 0.001 TYR J 305 ARG 0.002 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 916 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (t0) REVERT: A 939 ILE cc_start: 0.8308 (mm) cc_final: 0.8069 (mm) REVERT: A 945 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6481 (pm20) outliers start: 28 outliers final: 18 residues processed: 88 average time/residue: 0.1980 time to fit residues: 23.8089 Evaluate side-chains 84 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL 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: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6940 Z= 0.204 Angle : 0.556 10.414 9401 Z= 0.284 Chirality : 0.042 0.170 1085 Planarity : 0.003 0.039 1198 Dihedral : 4.581 20.380 915 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.19 % Allowed : 12.26 % Favored : 84.55 % 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: -1.22 (0.31), residues: 845 helix: 0.62 (0.36), residues: 231 sheet: -2.12 (0.42), residues: 159 loop : -1.02 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.015 0.001 PHE J 269 TYR 0.011 0.001 TYR J 305 ARG 0.002 0.000 ARG A 937 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.883 Fit side-chains REVERT: J 304 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6821 (tp30) REVERT: A 626 ARG cc_start: 0.6716 (tpt90) cc_final: 0.6445 (tpt-90) REVERT: A 700 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 939 ILE cc_start: 0.8237 (mm) cc_final: 0.8003 (mm) REVERT: A 945 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6453 (pm20) outliers start: 25 outliers final: 20 residues processed: 86 average time/residue: 0.1973 time to fit residues: 23.1794 Evaluate side-chains 86 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 257 GLN Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 15 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6940 Z= 0.177 Angle : 0.539 10.267 9401 Z= 0.276 Chirality : 0.041 0.172 1085 Planarity : 0.003 0.039 1198 Dihedral : 4.442 19.747 915 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.45 % Allowed : 12.77 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.31), residues: 845 helix: 0.73 (0.37), residues: 231 sheet: -2.09 (0.42), residues: 159 loop : -0.98 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.021 0.001 PHE J 269 TYR 0.010 0.001 TYR J 305 ARG 0.002 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.750 Fit side-chains REVERT: J 304 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6811 (tp30) REVERT: A 626 ARG cc_start: 0.6889 (tpt90) cc_final: 0.6615 (tpt-90) REVERT: A 939 ILE cc_start: 0.8167 (mm) cc_final: 0.7950 (mm) REVERT: A 945 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6505 (pm20) outliers start: 27 outliers final: 20 residues processed: 87 average time/residue: 0.1925 time to fit residues: 22.8876 Evaluate side-chains 83 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 257 GLN Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6940 Z= 0.180 Angle : 0.545 9.827 9401 Z= 0.278 Chirality : 0.041 0.169 1085 Planarity : 0.003 0.040 1198 Dihedral : 4.401 19.718 915 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.45 % Allowed : 13.15 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 845 helix: 0.79 (0.36), residues: 231 sheet: -2.08 (0.42), residues: 159 loop : -0.96 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.022 0.001 PHE J 269 TYR 0.009 0.001 TYR J 305 ARG 0.001 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 0.882 Fit side-chains REVERT: J 304 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6918 (tp30) REVERT: A 626 ARG cc_start: 0.6938 (tpt90) cc_final: 0.6641 (tpt-90) REVERT: A 699 ARG cc_start: 0.7886 (mmp-170) cc_final: 0.7460 (mmp-170) REVERT: A 700 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8057 (p0) REVERT: A 939 ILE cc_start: 0.8137 (mm) cc_final: 0.7916 (mm) REVERT: A 945 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6485 (pm20) outliers start: 27 outliers final: 24 residues processed: 83 average time/residue: 0.1987 time to fit residues: 22.5733 Evaluate side-chains 90 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 257 GLN Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.0030 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN A1006 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6940 Z= 0.230 Angle : 0.566 9.284 9401 Z= 0.288 Chirality : 0.042 0.170 1085 Planarity : 0.003 0.041 1198 Dihedral : 4.483 20.377 915 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.45 % Allowed : 13.41 % Favored : 83.14 % 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: -1.15 (0.31), residues: 845 helix: 0.76 (0.36), residues: 234 sheet: -2.13 (0.42), residues: 159 loop : -1.02 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.004 0.001 HIS A 913 PHE 0.022 0.001 PHE J 269 TYR 0.011 0.001 TYR J 305 ARG 0.002 0.000 ARG A 937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.810 Fit side-chains REVERT: J 304 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6943 (tp30) REVERT: A 602 ARG cc_start: 0.5346 (tpt170) cc_final: 0.4773 (tpt90) REVERT: A 699 ARG cc_start: 0.7936 (mmp-170) cc_final: 0.7497 (mmp-170) REVERT: A 700 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 939 ILE cc_start: 0.8234 (mm) cc_final: 0.8008 (mm) REVERT: A 945 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6502 (pm20) outliers start: 27 outliers final: 23 residues processed: 84 average time/residue: 0.1914 time to fit residues: 21.8747 Evaluate side-chains 89 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 258 CYS Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 276 TYR Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1080 CYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123681 restraints weight = 8308.226| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.55 r_work: 0.3452 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6940 Z= 0.172 Angle : 0.545 8.713 9401 Z= 0.278 Chirality : 0.041 0.174 1085 Planarity : 0.003 0.040 1198 Dihedral : 4.374 19.476 915 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.07 % Allowed : 13.92 % Favored : 83.01 % 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: -1.03 (0.31), residues: 845 helix: 0.87 (0.37), residues: 231 sheet: -2.11 (0.42), residues: 159 loop : -0.92 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 254 HIS 0.003 0.001 HIS A 913 PHE 0.023 0.001 PHE J 269 TYR 0.009 0.001 TYR J 305 ARG 0.002 0.000 ARG A 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.19 seconds wall clock time: 37 minutes 53.75 seconds (2273.75 seconds total)