Starting phenix.real_space_refine on Sat Mar 16 17:30:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/03_2024/8ier_35391_trim_updated.pdb" } resolution = 4.87 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= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 4851 2.51 5 N 1288 2.21 5 O 1309 1.98 5 H 7758 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 940": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15257 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 15243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 15243 Classifications: {'peptide': 967} Link IDs: {'CIS': 2, 'PTRANS': 62, 'TRANS': 902} Chain breaks: 9 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.09, per 1000 atoms: 0.46 Number of scatterers: 15257 At special positions: 0 Unit cell: (108, 113.4, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1309 8.00 N 1288 7.00 C 4851 6.00 H 7758 1.00 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: 11.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 5 sheets defined 40.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'P' and resid 51 through 57 Processing helix chain 'P' and resid 59 through 65 removed outlier: 3.561A pdb=" N LEU P 63 " --> pdb=" O GLY P 59 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU P 64 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE P 65 " --> pdb=" O PRO P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 59 through 65' Processing helix chain 'P' and resid 69 through 74 Processing helix chain 'P' and resid 196 through 200 Processing helix chain 'P' and resid 209 through 214 Processing helix chain 'P' and resid 228 through 237 removed outlier: 4.151A pdb=" N LEU P 237 " --> pdb=" O VAL P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 254 removed outlier: 3.731A pdb=" N GLN P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA P 253 " --> pdb=" O ALA P 249 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP P 254 " --> pdb=" O LEU P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 287 removed outlier: 3.640A pdb=" N GLN P 281 " --> pdb=" O LYS P 277 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER P 282 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG P 286 " --> pdb=" O SER P 282 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP P 287 " --> pdb=" O GLN P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 412 removed outlier: 3.654A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 450 removed outlier: 3.951A pdb=" N ILE P 441 " --> pdb=" O LEU P 437 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR P 442 " --> pdb=" O LEU P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 467 removed outlier: 3.914A pdb=" N ILE P 459 " --> pdb=" O ASN P 455 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA P 461 " --> pdb=" O ILE P 457 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 489 removed outlier: 4.035A pdb=" N LEU P 482 " --> pdb=" O THR P 478 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR P 483 " --> pdb=" O VAL P 479 " (cutoff:3.500A) Processing helix chain 'P' and resid 503 through 505 No H-bonds generated for 'chain 'P' and resid 503 through 505' Processing helix chain 'P' and resid 549 through 557 removed outlier: 3.724A pdb=" N THR P 557 " --> pdb=" O ARG P 553 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 581 Processing helix chain 'P' and resid 657 through 662 removed outlier: 3.767A pdb=" N GLY P 662 " --> pdb=" O GLU P 658 " (cutoff:3.500A) Processing helix chain 'P' and resid 675 through 681 Processing helix chain 'P' and resid 732 through 742 removed outlier: 3.841A pdb=" N THR P 742 " --> pdb=" O ALA P 738 " (cutoff:3.500A) Processing helix chain 'P' and resid 754 through 762 removed outlier: 3.584A pdb=" N THR P 759 " --> pdb=" O GLN P 755 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL P 760 " --> pdb=" O THR P 756 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 833 Processing helix chain 'P' and resid 837 through 839 No H-bonds generated for 'chain 'P' and resid 837 through 839' Processing helix chain 'P' and resid 842 through 845 No H-bonds generated for 'chain 'P' and resid 842 through 845' Processing helix chain 'P' and resid 856 through 869 removed outlier: 4.562A pdb=" N THR P 860 " --> pdb=" O GLU P 857 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU P 869 " --> pdb=" O LEU P 866 " (cutoff:3.500A) Processing helix chain 'P' and resid 883 through 887 Processing helix chain 'P' and resid 920 through 950 removed outlier: 3.758A pdb=" N CYS P 925 " --> pdb=" O ARG P 921 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER P 926 " --> pdb=" O GLU P 922 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR P 940 " --> pdb=" O TYR P 936 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR P 943 " --> pdb=" O LEU P 939 " (cutoff:3.500A) Processing helix chain 'P' and resid 960 through 970 removed outlier: 4.617A pdb=" N LEU P 964 " --> pdb=" O LEU P 961 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU P 968 " --> pdb=" O ALA P 965 " (cutoff:3.500A) Processing helix chain 'P' and resid 999 through 1025 removed outlier: 3.903A pdb=" N THR P1023 " --> pdb=" O GLY P1019 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU P1024 " --> pdb=" O TYR P1020 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1047 through 1064 Processing helix chain 'P' and resid 1079 through 1097 removed outlier: 3.517A pdb=" N LEU P1095 " --> pdb=" O VAL P1091 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL P1096 " --> pdb=" O LEU P1092 " (cutoff:3.500A) Processing helix chain 'P' and resid 1101 through 1106 Proline residue: P1105 - end of helix Processing helix chain 'P' and resid 1113 through 1115 No H-bonds generated for 'chain 'P' and resid 1113 through 1115' Processing helix chain 'P' and resid 1119 through 1147 removed outlier: 3.541A pdb=" N GLN P1140 " --> pdb=" O SER P1136 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS P1141 " --> pdb=" O VAL P1137 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU P1142 " --> pdb=" O LEU P1138 " (cutoff:3.500A) Proline residue: P1143 - end of helix Processing helix chain 'P' and resid 1157 through 1168 removed outlier: 3.858A pdb=" N LEU P1166 " --> pdb=" O LEU P1162 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA P1167 " --> pdb=" O GLU P1163 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU P1168 " --> pdb=" O ARG P1164 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 38 through 41 Processing sheet with id= B, first strand: chain 'P' and resid 103 through 105 removed outlier: 4.415A pdb=" N PHE P 103 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU P 167 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL P 105 " --> pdb=" O TYR P 165 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR P 165 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 294 through 298 Processing sheet with id= D, first strand: chain 'P' and resid 337 through 339 removed outlier: 3.609A pdb=" N GLN P 382 " --> pdb=" O MET P 339 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'P' and resid 717 through 720 removed outlier: 7.307A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 672 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: 4.77 Time building geometry restraints manager: 12.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7732 1.03 - 1.23: 27 1.23 - 1.42: 3047 1.42 - 1.62: 4535 1.62 - 1.81: 76 Bond restraints: 15417 Sorted by residual: bond pdb=" N ARG P 36 " pdb=" CA ARG P 36 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ARG P 36 " pdb=" H ARG P 36 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C PHE P 837 " pdb=" N PRO P 838 " ideal model delta sigma weight residual 1.334 1.346 -0.012 8.40e-03 1.42e+04 2.04e+00 bond pdb=" C12 SPM P1201 " pdb=" C13 SPM P1201 " ideal model delta sigma weight residual 1.527 1.502 0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C2 SPM P1201 " pdb=" C3 SPM P1201 " ideal model delta sigma weight residual 1.527 1.503 0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 15412 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 604 107.32 - 113.98: 18791 113.98 - 120.64: 4838 120.64 - 127.30: 3656 127.30 - 133.96: 99 Bond angle restraints: 27988 Sorted by residual: angle pdb=" C THR P 973 " pdb=" N VAL P 974 " pdb=" CA VAL P 974 " ideal model delta sigma weight residual 121.70 130.02 -8.32 1.80e+00 3.09e-01 2.13e+01 angle pdb=" C HIS P 836 " pdb=" N PHE P 837 " pdb=" CA PHE P 837 " ideal model delta sigma weight residual 120.09 125.71 -5.62 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C LEU P 518 " pdb=" N THR P 519 " pdb=" CA THR P 519 " ideal model delta sigma weight residual 121.70 126.93 -5.23 1.80e+00 3.09e-01 8.44e+00 angle pdb=" CB MET P 875 " pdb=" CG MET P 875 " pdb=" SD MET P 875 " ideal model delta sigma weight residual 112.70 119.24 -6.54 3.00e+00 1.11e-01 4.75e+00 angle pdb=" N ALA P 393 " pdb=" CA ALA P 393 " pdb=" C ALA P 393 " ideal model delta sigma weight residual 108.24 111.11 -2.87 1.32e+00 5.74e-01 4.71e+00 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6580 17.88 - 35.76: 474 35.76 - 53.64: 142 53.64 - 71.51: 37 71.51 - 89.39: 7 Dihedral angle restraints: 7240 sinusoidal: 4025 harmonic: 3215 Sorted by residual: dihedral pdb=" CA LYS P 835 " pdb=" C LYS P 835 " pdb=" N HIS P 836 " pdb=" CA HIS P 836 " ideal model delta harmonic sigma weight residual 180.00 -134.93 -45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA ILE P 215 " pdb=" C ILE P 215 " pdb=" N TYR P 216 " pdb=" CA TYR P 216 " ideal model delta harmonic sigma weight residual 180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 782 0.027 - 0.053: 288 0.053 - 0.080: 79 0.080 - 0.106: 66 0.106 - 0.133: 24 Chirality restraints: 1239 Sorted by residual: chirality pdb=" CA VAL P1030 " pdb=" N VAL P1030 " pdb=" C VAL P1030 " pdb=" CB VAL P1030 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE P 90 " pdb=" N ILE P 90 " pdb=" C ILE P 90 " pdb=" CB ILE P 90 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE P1111 " pdb=" N ILE P1111 " pdb=" C ILE P1111 " pdb=" CB ILE P1111 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1236 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR P 940 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR P 940 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR P 940 " 0.021 2.00e-02 2.50e+03 pdb=" N SER P 941 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P 473 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO P 474 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO P 474 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 474 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS P 68 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO P 69 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO P 69 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 69 " 0.019 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 572 2.16 - 2.77: 28920 2.77 - 3.38: 39651 3.38 - 3.99: 46502 3.99 - 4.60: 71637 Nonbonded interactions: 187282 Sorted by model distance: nonbonded pdb=" OE1 GLN P 675 " pdb=" H GLN P 675 " model vdw 1.546 1.850 nonbonded pdb=" O THR P 953 " pdb=" H ASN P 955 " model vdw 1.547 1.850 nonbonded pdb=" O THR P 402 " pdb=" H GLY P 406 " model vdw 1.620 1.850 nonbonded pdb=" OE1 GLU P 177 " pdb=" H GLU P 177 " model vdw 1.635 1.850 nonbonded pdb="HH22 ARG P 201 " pdb=" O ALA P 393 " model vdw 1.690 1.850 ... (remaining 187277 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=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: 0.010 Normalize map: mean=0, sd=1: 2.670 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: 0.260 Extract box with map and model: 6.630 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.140 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 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 : 0.002 0.033 7659 Z= 0.136 Angle : 0.529 8.316 10416 Z= 0.265 Chirality : 0.038 0.133 1239 Planarity : 0.003 0.034 1303 Dihedral : 12.911 89.393 2815 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.39 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.61 (0.30), residues: 947 helix: 1.69 (0.30), residues: 372 sheet: 1.03 (0.83), residues: 46 loop : -2.26 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP P 251 HIS 0.002 0.000 HIS P 836 PHE 0.008 0.001 PHE P 428 TYR 0.016 0.001 TYR P1058 ARG 0.004 0.000 ARG P 783 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 957 ASN cc_start: 0.7742 (p0) cc_final: 0.7438 (p0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3520 time to fit residues: 51.1851 Evaluate side-chains 86 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4953 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7659 Z= 0.164 Angle : 0.506 5.448 10416 Z= 0.257 Chirality : 0.038 0.148 1239 Planarity : 0.003 0.034 1303 Dihedral : 3.937 54.164 1057 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.50 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.90 (0.29), residues: 947 helix: 1.21 (0.29), residues: 382 sheet: 0.77 (0.82), residues: 46 loop : -2.28 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP P 306 HIS 0.002 0.000 HIS P 822 PHE 0.020 0.001 PHE P1132 TYR 0.012 0.001 TYR P 483 ARG 0.002 0.000 ARG P 783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 103 PHE cc_start: 0.6613 (t80) cc_final: 0.6400 (t80) REVERT: P 231 LEU cc_start: 0.6610 (tp) cc_final: 0.6396 (tp) REVERT: P 753 ASN cc_start: 0.6954 (t0) cc_final: 0.6102 (t0) REVERT: P 957 ASN cc_start: 0.8186 (p0) cc_final: 0.7821 (p0) REVERT: P 1061 LEU cc_start: 0.7633 (tt) cc_final: 0.7252 (tp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3468 time to fit residues: 52.8974 Evaluate side-chains 87 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7659 Z= 0.163 Angle : 0.515 5.326 10416 Z= 0.259 Chirality : 0.038 0.156 1239 Planarity : 0.004 0.036 1303 Dihedral : 4.099 50.293 1057 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.24 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.89 (0.29), residues: 947 helix: 1.37 (0.30), residues: 375 sheet: 0.71 (0.82), residues: 46 loop : -2.36 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 643 HIS 0.002 0.001 HIS P 822 PHE 0.014 0.001 PHE P 400 TYR 0.012 0.001 TYR P 216 ARG 0.002 0.000 ARG P 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.6861 (tp) cc_final: 0.6633 (tp) REVERT: P 672 ASP cc_start: 0.8346 (t0) cc_final: 0.8127 (t0) REVERT: P 753 ASN cc_start: 0.7305 (t0) cc_final: 0.6432 (t0) REVERT: P 940 TYR cc_start: 0.7556 (t80) cc_final: 0.7259 (t80) REVERT: P 1061 LEU cc_start: 0.7652 (tt) cc_final: 0.7237 (tp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3551 time to fit residues: 52.0585 Evaluate side-chains 86 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 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 : 0.003 0.083 7659 Z= 0.214 Angle : 0.538 5.203 10416 Z= 0.274 Chirality : 0.038 0.155 1239 Planarity : 0.005 0.123 1303 Dihedral : 4.177 46.827 1057 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.98 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.29), residues: 947 helix: 1.14 (0.29), residues: 381 sheet: 0.59 (0.80), residues: 46 loop : -2.38 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 251 HIS 0.004 0.001 HIS P 772 PHE 0.025 0.001 PHE P1132 TYR 0.012 0.001 TYR P1045 ARG 0.008 0.000 ARG P 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.6951 (tp) cc_final: 0.6713 (tp) REVERT: P 308 ASP cc_start: 0.7974 (p0) cc_final: 0.7476 (p0) REVERT: P 753 ASN cc_start: 0.7573 (t0) cc_final: 0.6590 (t0) REVERT: P 1061 LEU cc_start: 0.7815 (tt) cc_final: 0.7523 (tp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3445 time to fit residues: 52.1653 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 31 optimal weight: 9.9990 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 101 GLN ** P 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7659 Z= 0.246 Angle : 0.653 8.244 10416 Z= 0.340 Chirality : 0.041 0.212 1239 Planarity : 0.005 0.049 1303 Dihedral : 4.995 42.081 1057 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.77 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.61 (0.28), residues: 947 helix: 0.58 (0.28), residues: 374 sheet: -0.46 (0.60), residues: 65 loop : -2.58 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 643 HIS 0.004 0.001 HIS P 626 PHE 0.025 0.002 PHE P1132 TYR 0.020 0.002 TYR P1045 ARG 0.015 0.001 ARG P 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7231 (tp) cc_final: 0.7003 (tp) REVERT: P 293 MET cc_start: -0.3567 (ptt) cc_final: -0.3888 (ptt) REVERT: P 394 VAL cc_start: 0.8913 (m) cc_final: 0.8586 (m) REVERT: P 753 ASN cc_start: 0.8143 (t0) cc_final: 0.7228 (t0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3467 time to fit residues: 54.7602 Evaluate side-chains 90 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7659 Z= 0.156 Angle : 0.531 4.895 10416 Z= 0.269 Chirality : 0.039 0.180 1239 Planarity : 0.004 0.048 1303 Dihedral : 4.503 40.525 1057 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.19 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.33 (0.29), residues: 947 helix: 0.96 (0.29), residues: 370 sheet: -0.50 (0.60), residues: 65 loop : -2.49 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 251 HIS 0.003 0.001 HIS P 190 PHE 0.027 0.002 PHE P1029 TYR 0.014 0.001 TYR P 940 ARG 0.003 0.000 ARG P 991 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7169 (tp) cc_final: 0.6915 (tp) REVERT: P 277 LYS cc_start: 0.5660 (mttt) cc_final: 0.4930 (mmtp) REVERT: P 481 THR cc_start: 0.8404 (p) cc_final: 0.8154 (p) REVERT: P 753 ASN cc_start: 0.7956 (t0) cc_final: 0.7018 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3372 time to fit residues: 53.7856 Evaluate side-chains 91 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.0000 chunk 51 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 55 optimal weight: 0.2980 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1047 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7659 Z= 0.136 Angle : 0.505 4.826 10416 Z= 0.252 Chirality : 0.039 0.165 1239 Planarity : 0.004 0.048 1303 Dihedral : 4.144 38.550 1057 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.87 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.07 (0.29), residues: 947 helix: 1.20 (0.30), residues: 366 sheet: -0.26 (0.70), residues: 55 loop : -2.31 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 643 HIS 0.005 0.001 HIS P 772 PHE 0.015 0.001 PHE P 963 TYR 0.012 0.001 TYR P1045 ARG 0.003 0.000 ARG P 821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7236 (tp) cc_final: 0.6995 (tp) REVERT: P 277 LYS cc_start: 0.5679 (mttt) cc_final: 0.4938 (mmtp) REVERT: P 308 ASP cc_start: 0.8467 (p0) cc_final: 0.7935 (p0) REVERT: P 477 MET cc_start: 0.7310 (pmm) cc_final: 0.6439 (mtp) REVERT: P 753 ASN cc_start: 0.7827 (t0) cc_final: 0.6905 (t0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3369 time to fit residues: 52.0816 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 8 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7659 Z= 0.146 Angle : 0.506 4.865 10416 Z= 0.255 Chirality : 0.039 0.156 1239 Planarity : 0.004 0.048 1303 Dihedral : 4.110 38.082 1057 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.29 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.29), residues: 947 helix: 1.21 (0.30), residues: 371 sheet: -0.21 (0.70), residues: 55 loop : -2.26 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P1028 HIS 0.002 0.001 HIS P 190 PHE 0.013 0.001 PHE P 963 TYR 0.011 0.001 TYR P 216 ARG 0.002 0.000 ARG P 853 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7253 (tp) cc_final: 0.6983 (tp) REVERT: P 277 LYS cc_start: 0.5725 (mttt) cc_final: 0.5064 (mmtp) REVERT: P 477 MET cc_start: 0.7402 (pmm) cc_final: 0.6518 (mtp) REVERT: P 940 TYR cc_start: 0.8341 (t80) cc_final: 0.7544 (t80) REVERT: P 1029 PHE cc_start: 0.7365 (m-80) cc_final: 0.7094 (t80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3367 time to fit residues: 50.9461 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 244 GLN ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7659 Z= 0.156 Angle : 0.523 4.901 10416 Z= 0.263 Chirality : 0.039 0.165 1239 Planarity : 0.004 0.051 1303 Dihedral : 4.198 37.475 1057 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.24 % Favored : 89.44 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.09 (0.29), residues: 947 helix: 1.15 (0.29), residues: 371 sheet: -0.24 (0.60), residues: 65 loop : -2.36 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 643 HIS 0.003 0.001 HIS P 372 PHE 0.019 0.001 PHE P 963 TYR 0.010 0.001 TYR P 216 ARG 0.002 0.000 ARG P 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7167 (tp) cc_final: 0.6919 (tp) REVERT: P 277 LYS cc_start: 0.6274 (mttt) cc_final: 0.5633 (mmtp) REVERT: P 477 MET cc_start: 0.7536 (pmm) cc_final: 0.6603 (mtp) REVERT: P 940 TYR cc_start: 0.8405 (t80) cc_final: 0.7715 (t80) REVERT: P 1030 VAL cc_start: 0.7512 (t) cc_final: 0.7101 (p) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.3063 time to fit residues: 46.5380 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7659 Z= 0.155 Angle : 0.521 4.883 10416 Z= 0.262 Chirality : 0.039 0.156 1239 Planarity : 0.004 0.049 1303 Dihedral : 4.208 37.014 1057 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.61 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.29), residues: 947 helix: 1.08 (0.29), residues: 371 sheet: -0.23 (0.59), residues: 65 loop : -2.39 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 583 HIS 0.002 0.001 HIS P 190 PHE 0.028 0.001 PHE P1116 TYR 0.010 0.001 TYR P 216 ARG 0.002 0.000 ARG P1034 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 231 LEU cc_start: 0.7169 (tp) cc_final: 0.6908 (tp) REVERT: P 277 LYS cc_start: 0.6288 (mttt) cc_final: 0.5646 (mmtp) REVERT: P 477 MET cc_start: 0.7535 (pmm) cc_final: 0.6589 (mtp) REVERT: P 940 TYR cc_start: 0.8406 (t80) cc_final: 0.7765 (t80) REVERT: P 1030 VAL cc_start: 0.7707 (t) cc_final: 0.7271 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3523 time to fit residues: 53.5967 Evaluate side-chains 89 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.158833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.141805 restraints weight = 88077.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.146145 restraints weight = 55754.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.148319 restraints weight = 37065.190| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7659 Z= 0.134 Angle : 0.495 4.809 10416 Z= 0.246 Chirality : 0.038 0.156 1239 Planarity : 0.004 0.047 1303 Dihedral : 4.024 35.627 1057 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.45 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.29), residues: 947 helix: 1.15 (0.30), residues: 373 sheet: -0.18 (0.68), residues: 55 loop : -2.26 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 643 HIS 0.002 0.000 HIS P 190 PHE 0.014 0.001 PHE P 963 TYR 0.012 0.001 TYR P1058 ARG 0.002 0.000 ARG P 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3239.78 seconds wall clock time: 57 minutes 36.75 seconds (3456.75 seconds total)