Starting phenix.real_space_refine on Fri Sep 27 09:03:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/09_2024/8ier_35391_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/09_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_35391/09_2024/8ier_35391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/09_2024/8ier_35391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/09_2024/8ier_35391_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ier_35391/09_2024/8ier_35391_trim.cif" } 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. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.19, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 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: 4.54 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 38 helices and 10 sheets defined 46.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'P' and resid 50 through 58 Processing helix chain 'P' and resid 58 through 63 removed outlier: 3.693A pdb=" N LEU P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU P 63 " --> pdb=" O GLY P 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 63' Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 70 through 75 Processing helix chain 'P' and resid 195 through 201 Processing helix chain 'P' and resid 208 through 215 removed outlier: 3.548A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 236 Processing helix chain 'P' and resid 238 through 253 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) Processing helix chain 'P' and resid 257 through 286 removed outlier: 4.244A pdb=" N CYS P 262 " --> pdb=" O TRP P 258 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE P 263 " --> pdb=" O TYR P 259 " (cutoff:3.500A) 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) Processing helix chain 'P' and resid 402 through 413 removed outlier: 3.654A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 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 454 through 468 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 477 through 490 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 502 through 506 removed outlier: 4.182A pdb=" N LYS P 506 " --> pdb=" O LEU P 503 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 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 582 Processing helix chain 'P' and resid 643 through 646 Processing helix chain 'P' and resid 656 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 674 through 682 Processing helix chain 'P' and resid 731 through 741 removed outlier: 4.093A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 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 826 through 834 removed outlier: 3.532A pdb=" N PHE P 830 " --> pdb=" O SER P 826 " (cutoff:3.500A) Processing helix chain 'P' and resid 836 through 840 removed outlier: 3.612A pdb=" N LEU P 840 " --> pdb=" O PHE P 837 " (cutoff:3.500A) Processing helix chain 'P' and resid 841 through 846 removed outlier: 3.708A pdb=" N LEU P 845 " --> pdb=" O LEU P 841 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL P 846 " --> pdb=" O PRO P 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 841 through 846' Processing helix chain 'P' and resid 855 through 857 No H-bonds generated for 'chain 'P' and resid 855 through 857' Processing helix chain 'P' and resid 858 through 868 Processing helix chain 'P' and resid 882 through 888 Processing helix chain 'P' and resid 919 through 951 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 959 through 962 Processing helix chain 'P' and resid 963 through 971 removed outlier: 3.516A pdb=" N ASP P 967 " --> pdb=" O PHE P 963 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL P 969 " --> pdb=" O ALA P 965 " (cutoff:3.500A) Processing helix chain 'P' and resid 998 through 1022 Processing helix chain 'P' and resid 1023 through 1026 Processing helix chain 'P' and resid 1046 through 1066 removed outlier: 3.628A pdb=" N SER P1066 " --> pdb=" O ALA P1062 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1098 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) removed outlier: 3.529A pdb=" N VAL P1098 " --> pdb=" O GLY P1094 " (cutoff:3.500A) Processing helix chain 'P' and resid 1102 through 1107 removed outlier: 3.779A pdb=" N LEU P1106 " --> pdb=" O LEU P1102 " (cutoff:3.500A) Processing helix chain 'P' and resid 1112 through 1116 removed outlier: 3.520A pdb=" N PHE P1116 " --> pdb=" O ASP P1113 " (cutoff:3.500A) Processing helix chain 'P' and resid 1118 through 1148 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 1156 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=AA1, first strand: chain 'P' and resid 39 through 41 Processing sheet with id=AA2, 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=AA3, first strand: chain 'P' and resid 294 through 298 Processing sheet with id=AA4, first strand: chain 'P' and resid 373 through 374 removed outlier: 3.515A pdb=" N ALA P 331 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, first strand: chain 'P' and resid 509 through 510 Processing sheet with id=AA7, first strand: chain 'P' and resid 524 through 525 removed outlier: 3.692A pdb=" N ASP P 524 " --> pdb=" O ARG P 725 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG P 725 " --> pdb=" O ASP P 524 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET P 724 " --> pdb=" O ARG P 686 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG P 686 " --> pdb=" O MET P 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'P' and resid 624 through 627 removed outlier: 7.307A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 772 through 773 removed outlier: 7.486A pdb=" N HIS P 772 " --> pdb=" O ALA P 824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'P' and resid 875 through 876 removed outlier: 6.118A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 286 hydrogen bonds defined for protein. 810 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: 5.44 Time building geometry restraints manager: 5.30 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: 0.00 - 1.66: 27656 1.66 - 3.33: 288 3.33 - 4.99: 37 4.99 - 6.65: 6 6.65 - 8.32: 1 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: 549 2.16 - 2.77: 28897 2.77 - 3.38: 39620 3.38 - 3.99: 46441 3.99 - 4.60: 71592 Nonbonded interactions: 187099 Sorted by model distance: nonbonded pdb=" OE1 GLN P 675 " pdb=" H GLN P 675 " model vdw 1.546 2.450 nonbonded pdb=" O THR P 953 " pdb=" H ASN P 955 " model vdw 1.547 2.450 nonbonded pdb=" OE1 GLU P 177 " pdb=" H GLU P 177 " model vdw 1.635 2.450 nonbonded pdb="HH22 ARG P 201 " pdb=" O ALA P 393 " model vdw 1.690 2.450 nonbonded pdb=" O PRO P1074 " pdb=" HG1 THR P1077 " model vdw 1.701 2.450 ... (remaining 187094 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: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.290 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- 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= 0.131 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 : 1.088 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: 0.3533 time to fit residues: 51.3589 Evaluate side-chains 86 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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: 0.7980 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.4840 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7659 Z= 0.148 Angle : 0.512 5.730 10416 Z= 0.261 Chirality : 0.038 0.147 1239 Planarity : 0.003 0.035 1303 Dihedral : 3.929 56.212 1057 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.81 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.67 (0.29), residues: 947 helix: 1.61 (0.30), residues: 374 sheet: 0.92 (0.82), residues: 46 loop : -2.28 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP P 306 HIS 0.002 0.000 HIS P 190 PHE 0.040 0.001 PHE P1132 TYR 0.011 0.001 TYR P 216 ARG 0.002 0.000 ARG P 78 *********************** 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 103 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.204 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 231 LEU cc_start: 0.6617 (tp) cc_final: 0.6409 (tp) REVERT: P 477 MET cc_start: 0.7104 (pmm) cc_final: 0.5921 (mmm) REVERT: P 957 ASN cc_start: 0.7950 (p0) cc_final: 0.7345 (p0) REVERT: P 1061 LEU cc_start: 0.7643 (tt) cc_final: 0.7254 (tp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3406 time to fit residues: 50.6783 Evaluate side-chains 84 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 7.9990 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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: 0.5003 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7659 Z= 0.156 Angle : 0.519 5.727 10416 Z= 0.264 Chirality : 0.039 0.149 1239 Planarity : 0.004 0.035 1303 Dihedral : 4.060 50.436 1057 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.34 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.72 (0.29), residues: 947 helix: 1.66 (0.29), residues: 372 sheet: 0.69 (0.80), residues: 46 loop : -2.36 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 643 HIS 0.002 0.001 HIS P 822 PHE 0.019 0.001 PHE P 400 TYR 0.014 0.001 TYR P 216 ARG 0.005 0.000 ARG P 78 *********************** 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 105 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.645 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 210 MET cc_start: -0.2848 (tpt) cc_final: -0.4627 (tmm) REVERT: P 231 LEU cc_start: 0.6645 (tp) cc_final: 0.6376 (tp) REVERT: P 477 MET cc_start: 0.6633 (pmm) cc_final: 0.6046 (mmm) REVERT: P 957 ASN cc_start: 0.8215 (p0) cc_final: 0.7861 (p0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3935 time to fit residues: 59.1832 Evaluate side-chains 83 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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: 0.5086 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7659 Z= 0.158 Angle : 0.531 5.587 10416 Z= 0.271 Chirality : 0.038 0.148 1239 Planarity : 0.004 0.079 1303 Dihedral : 4.066 47.571 1057 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.87 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.72 (0.29), residues: 947 helix: 1.66 (0.29), residues: 372 sheet: 0.76 (0.81), residues: 46 loop : -2.36 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 643 HIS 0.004 0.001 HIS P 772 PHE 0.034 0.001 PHE P1132 TYR 0.014 0.001 TYR P 216 ARG 0.006 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 103 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 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 210 MET cc_start: -0.3023 (tpt) cc_final: -0.4703 (tmm) REVERT: P 231 LEU cc_start: 0.6648 (tp) cc_final: 0.6438 (tp) REVERT: P 477 MET cc_start: 0.6726 (pmm) cc_final: 0.6143 (mmm) REVERT: P 753 ASN cc_start: 0.6982 (t0) cc_final: 0.6236 (t0) REVERT: P 875 MET cc_start: 0.8308 (tpp) cc_final: 0.8032 (mmm) REVERT: P 957 ASN cc_start: 0.8322 (p0) cc_final: 0.7725 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3588 time to fit residues: 52.6874 Evaluate side-chains 86 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 23 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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: 0.5104 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7659 Z= 0.134 Angle : 0.506 5.540 10416 Z= 0.256 Chirality : 0.039 0.145 1239 Planarity : 0.004 0.034 1303 Dihedral : 3.968 43.607 1057 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.76 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.67 (0.29), residues: 947 helix: 1.68 (0.29), residues: 374 sheet: 0.78 (0.82), residues: 46 loop : -2.32 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 100 HIS 0.002 0.000 HIS P 190 PHE 0.026 0.001 PHE P1132 TYR 0.013 0.001 TYR P 216 ARG 0.002 0.000 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 : 1.172 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: P 210 MET cc_start: -0.2825 (tpt) cc_final: -0.4607 (tmm) REVERT: P 231 LEU cc_start: 0.6909 (tp) cc_final: 0.6634 (tp) REVERT: P 308 ASP cc_start: 0.7972 (p0) cc_final: 0.7460 (p0) REVERT: P 394 VAL cc_start: 0.8942 (m) cc_final: 0.8230 (m) REVERT: P 477 MET cc_start: 0.6734 (pmm) cc_final: 0.6190 (mmm) REVERT: P 748 MET cc_start: 0.7013 (ptp) cc_final: 0.5326 (ptm) REVERT: P 753 ASN cc_start: 0.6928 (t0) cc_final: 0.6166 (t0) REVERT: P 875 MET cc_start: 0.8467 (tpp) cc_final: 0.8195 (mmm) REVERT: P 957 ASN cc_start: 0.8272 (p0) cc_final: 0.7718 (p0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3480 time to fit residues: 54.6654 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.0270 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- 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: 0.5231 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7659 Z= 0.167 Angle : 0.531 5.596 10416 Z= 0.271 Chirality : 0.039 0.152 1239 Planarity : 0.004 0.036 1303 Dihedral : 4.074 42.772 1057 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.66 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.68 (0.29), residues: 947 helix: 1.72 (0.29), residues: 373 sheet: 0.68 (0.80), residues: 46 loop : -2.36 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 100 HIS 0.002 0.001 HIS P 822 PHE 0.029 0.002 PHE P1116 TYR 0.014 0.001 TYR P 216 ARG 0.006 0.000 ARG P 201 *********************** 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 104 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.272 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 210 MET cc_start: -0.2907 (tpt) cc_final: -0.4922 (tmm) REVERT: P 231 LEU cc_start: 0.6959 (tp) cc_final: 0.6681 (tp) REVERT: P 308 ASP cc_start: 0.8002 (p0) cc_final: 0.7515 (p0) REVERT: P 477 MET cc_start: 0.6992 (pmm) cc_final: 0.6350 (mmm) REVERT: P 753 ASN cc_start: 0.7110 (t0) cc_final: 0.6370 (t0) REVERT: P 957 ASN cc_start: 0.8561 (p0) cc_final: 0.7984 (p0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3465 time to fit residues: 52.8412 Evaluate side-chains 85 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7659 Z= 0.194 Angle : 0.575 5.556 10416 Z= 0.298 Chirality : 0.040 0.160 1239 Planarity : 0.004 0.041 1303 Dihedral : 4.298 42.682 1057 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.82 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -0.83 (0.29), residues: 947 helix: 1.52 (0.29), residues: 377 sheet: 0.13 (0.62), residues: 65 loop : -2.44 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 583 HIS 0.003 0.001 HIS P 198 PHE 0.014 0.002 PHE P 103 TYR 0.016 0.002 TYR P 940 ARG 0.006 0.001 ARG P 201 *********************** 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 100 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.279 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 210 MET cc_start: -0.2592 (tpt) cc_final: -0.4588 (tmm) REVERT: P 231 LEU cc_start: 0.7102 (tp) cc_final: 0.6844 (tp) REVERT: P 293 MET cc_start: -0.3502 (ptt) cc_final: -0.3874 (ptt) REVERT: P 308 ASP cc_start: 0.8421 (p0) cc_final: 0.7909 (p0) REVERT: P 477 MET cc_start: 0.7322 (pmm) cc_final: 0.6437 (mmm) REVERT: P 576 LYS cc_start: 0.8464 (tptp) cc_final: 0.8086 (tptp) REVERT: P 748 MET cc_start: 0.6955 (ptp) cc_final: 0.5350 (ptm) REVERT: P 753 ASN cc_start: 0.7538 (t0) cc_final: 0.6713 (t0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3482 time to fit residues: 50.2739 Evaluate side-chains 84 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.0370 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- 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: 0.5405 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7659 Z= 0.146 Angle : 0.522 5.413 10416 Z= 0.266 Chirality : 0.039 0.137 1239 Planarity : 0.004 0.043 1303 Dihedral : 4.110 41.255 1057 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.08 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.71 (0.29), residues: 947 helix: 1.62 (0.29), residues: 371 sheet: 0.10 (0.61), residues: 65 loop : -2.31 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 251 HIS 0.002 0.001 HIS P 190 PHE 0.029 0.002 PHE P1029 TYR 0.012 0.001 TYR P 216 ARG 0.009 0.000 ARG P 740 *********************** 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 101 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.195 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: P 210 MET cc_start: -0.2689 (tpt) cc_final: -0.4400 (tmm) REVERT: P 231 LEU cc_start: 0.7122 (tp) cc_final: 0.6878 (tp) REVERT: P 293 MET cc_start: -0.3373 (ptt) cc_final: -0.3760 (ptt) REVERT: P 308 ASP cc_start: 0.8363 (p0) cc_final: 0.7850 (p0) REVERT: P 477 MET cc_start: 0.7176 (pmm) cc_final: 0.6144 (mmm) REVERT: P 748 MET cc_start: 0.7030 (ptp) cc_final: 0.5324 (ptm) REVERT: P 753 ASN cc_start: 0.7478 (t0) cc_final: 0.6649 (t0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3263 time to fit residues: 48.3075 Evaluate side-chains 88 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.0050 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.5446 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7659 Z= 0.142 Angle : 0.520 5.449 10416 Z= 0.266 Chirality : 0.039 0.184 1239 Planarity : 0.004 0.057 1303 Dihedral : 4.023 40.518 1057 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.50 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.69 (0.29), residues: 947 helix: 1.69 (0.29), residues: 366 sheet: 0.06 (0.61), residues: 65 loop : -2.30 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 71 HIS 0.009 0.001 HIS P 772 PHE 0.029 0.001 PHE P1128 TYR 0.012 0.001 TYR P 216 ARG 0.006 0.000 ARG P 740 *********************** 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 102 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.195 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: P 210 MET cc_start: -0.2677 (tpt) cc_final: -0.4606 (tmm) REVERT: P 231 LEU cc_start: 0.7131 (tp) cc_final: 0.6887 (tp) REVERT: P 293 MET cc_start: -0.3464 (ptt) cc_final: -0.3847 (ptt) REVERT: P 308 ASP cc_start: 0.8417 (p0) cc_final: 0.7909 (p0) REVERT: P 477 MET cc_start: 0.7231 (pmm) cc_final: 0.6276 (mmm) REVERT: P 748 MET cc_start: 0.7156 (ptp) cc_final: 0.5489 (ptm) REVERT: P 753 ASN cc_start: 0.7527 (t0) cc_final: 0.6715 (t0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3188 time to fit residues: 47.9705 Evaluate side-chains 87 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.5610 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7659 Z= 0.184 Angle : 0.565 5.490 10416 Z= 0.292 Chirality : 0.039 0.153 1239 Planarity : 0.004 0.056 1303 Dihedral : 4.283 40.805 1057 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.61 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.97 (0.29), residues: 947 helix: 1.32 (0.29), residues: 377 sheet: -0.07 (0.61), residues: 65 loop : -2.43 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 583 HIS 0.004 0.001 HIS P 255 PHE 0.018 0.002 PHE P 963 TYR 0.014 0.001 TYR P1045 ARG 0.004 0.000 ARG P 78 ********************** 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 101 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.318 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 210 MET cc_start: -0.2474 (tpt) cc_final: -0.4585 (tmm) REVERT: P 231 LEU cc_start: 0.7139 (tp) cc_final: 0.6893 (tp) REVERT: P 293 MET cc_start: -0.3543 (ptt) cc_final: -0.3756 (ptt) REVERT: P 477 MET cc_start: 0.7463 (pmm) cc_final: 0.6504 (mmm) REVERT: P 748 MET cc_start: 0.7239 (ptp) cc_final: 0.5568 (ptm) REVERT: P 875 MET cc_start: 0.8745 (tpp) cc_final: 0.8450 (tpp) REVERT: P 1113 ASP cc_start: 0.5595 (m-30) cc_final: 0.5355 (m-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3319 time to fit residues: 49.2894 Evaluate side-chains 84 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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: 0.1980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.160511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.143144 restraints weight = 87835.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.147042 restraints weight = 55371.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.149806 restraints weight = 37287.073| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.4032 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= 0.145 Angle : 0.524 5.409 10416 Z= 0.268 Chirality : 0.039 0.156 1239 Planarity : 0.004 0.054 1303 Dihedral : 4.149 39.467 1057 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.40 % Favored : 90.39 % 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: -0.89 (0.29), residues: 947 helix: 1.41 (0.29), residues: 377 sheet: -0.04 (0.60), residues: 65 loop : -2.39 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 643 HIS 0.003 0.001 HIS P 255 PHE 0.026 0.002 PHE P1128 TYR 0.011 0.001 TYR P1058 ARG 0.004 0.000 ARG P 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.85 seconds wall clock time: 57 minutes 8.35 seconds (3428.35 seconds total)