Starting phenix.real_space_refine on Thu Feb 15 04:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/02_2024/8atv_15664_updated.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 P 61 5.49 5 S 35 5.16 5 C 6950 2.51 5 N 1943 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 212": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 1272": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11161 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2733 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 314} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 7199 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Conformer: "B" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 bond proxies already assigned to first conformer: 7343 Chain: "N" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 4} Link IDs: {'rna3p': 3} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.84 Number of scatterers: 11161 At special positions: 0 Unit cell: (102.82, 117.37, 119.31, 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 35 16.00 P 61 15.00 O 2172 8.00 N 1943 7.00 C 6950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 3.6 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 9 sheets defined 50.0% alpha, 7.9% beta 21 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.567A pdb=" N LYS B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 105 through 112 removed outlier: 3.953A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 420 removed outlier: 4.088A pdb=" N GLN A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 440 Processing helix chain 'A' and resid 449 through 477 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.820A pdb=" N THR A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 518 Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.645A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 Processing helix chain 'A' and resid 653 through 659 removed outlier: 4.207A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 776 through 812 removed outlier: 3.500A pdb=" N THR A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 914 through 928 Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 978 through 993 Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.145A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1037 removed outlier: 3.687A pdb=" N GLN A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1065 Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1091 through 1093 No H-bonds generated for 'chain 'A' and resid 1091 through 1093' Processing helix chain 'A' and resid 1150 through 1179 Proline residue: A1158 - end of helix removed outlier: 3.629A pdb=" N ILE A1162 " --> pdb=" O PRO A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1217 through 1228 Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.596A pdb=" N ILE A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1280 removed outlier: 3.581A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.506A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 200 through 207 removed outlier: 6.680A pdb=" N LEU B 244 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE B 207 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 242 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 49 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL B 135 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 51 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN B 137 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 53 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 72 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP B 52 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER B 74 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 96 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 530 Processing sheet with id= C, first strand: chain 'A' and resid 613 through 619 removed outlier: 3.637A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= E, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= F, first strand: chain 'A' and resid 942 through 945 Processing sheet with id= G, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= H, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.521A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1233 through 1238 removed outlier: 3.546A pdb=" N LEU A1238 " --> pdb=" O MET A1321 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A1321 " --> pdb=" O LEU A1238 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3129 1.34 - 1.45: 2167 1.45 - 1.57: 6081 1.57 - 1.69: 112 1.69 - 1.81: 59 Bond restraints: 11548 Sorted by residual: bond pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.50e-02 4.44e+03 8.26e+01 bond pdb=" O3' DA T 13 " pdb=" P DT T 14 " ideal model delta sigma weight residual 1.607 1.494 0.113 1.50e-02 4.44e+03 5.67e+01 bond pdb=" O3' DC T 25 " pdb=" P DA T 26 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 1.607 1.687 -0.080 1.50e-02 4.44e+03 2.86e+01 bond pdb=" O3' DA N 133 " pdb=" P DT N 134 " ideal model delta sigma weight residual 1.607 1.528 0.079 1.50e-02 4.44e+03 2.77e+01 ... (remaining 11543 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 623 106.15 - 113.13: 6271 113.13 - 120.11: 4007 120.11 - 127.09: 4718 127.09 - 134.06: 295 Bond angle restraints: 15914 Sorted by residual: angle pdb=" C5' DA N 130 " pdb=" C4' DA N 130 " pdb=" O4' DA N 130 " ideal model delta sigma weight residual 109.40 117.79 -8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C5' DT T 34 " pdb=" C4' DT T 34 " pdb=" O4' DT T 34 " ideal model delta sigma weight residual 109.40 116.99 -7.59 1.50e+00 4.44e-01 2.56e+01 angle pdb=" C LEU A 755 " pdb=" CA LEU A 755 " pdb=" CB LEU A 755 " ideal model delta sigma weight residual 117.23 110.74 6.49 1.36e+00 5.41e-01 2.28e+01 angle pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 120.20 127.00 -6.80 1.50e+00 4.44e-01 2.06e+01 angle pdb=" C3' DT N 112 " pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 120.20 126.82 -6.62 1.50e+00 4.44e-01 1.95e+01 ... (remaining 15909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 6265 27.58 - 55.17: 488 55.17 - 82.75: 51 82.75 - 110.34: 6 110.34 - 137.92: 2 Dihedral angle restraints: 6812 sinusoidal: 3137 harmonic: 3675 Sorted by residual: dihedral pdb=" O3A GTP C 201 " pdb=" O3B GTP C 201 " pdb=" PB GTP C 201 " pdb=" PG GTP C 201 " ideal model delta sinusoidal sigma weight residual 303.79 165.87 137.92 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -12.68 117.28 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" O3B GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PB GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual -68.92 -166.09 97.17 1 2.00e+01 2.50e-03 2.70e+01 ... (remaining 6809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1711 0.106 - 0.212: 45 0.212 - 0.318: 3 0.318 - 0.424: 2 0.424 - 0.530: 1 Chirality restraints: 1762 Sorted by residual: chirality pdb=" P DT N 127 " pdb=" OP1 DT N 127 " pdb=" OP2 DT N 127 " pdb=" O5' DT N 127 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C4' DA N 130 " pdb=" C5' DA N 130 " pdb=" O4' DA N 130 " pdb=" C3' DA N 130 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' DG N 108 " pdb=" C4' DG N 108 " pdb=" O3' DG N 108 " pdb=" C2' DG N 108 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1759 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 120 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 703 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 704 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 775 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 776 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 776 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 776 " 0.022 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 401 2.72 - 3.26: 10665 3.26 - 3.81: 19067 3.81 - 4.35: 23215 4.35 - 4.90: 38377 Nonbonded interactions: 91725 Sorted by model distance: nonbonded pdb=" O ASN A 487 " pdb=" OG1 THR A 491 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASP B 257 " pdb=" N ASN B 258 " model vdw 2.177 2.520 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.214 2.440 nonbonded pdb=" NE2 GLN A 416 " pdb=" OE1 GLU A 420 " model vdw 2.261 2.520 nonbonded pdb=" O PHE B 90 " pdb=" OG SER B 93 " model vdw 2.264 2.440 ... (remaining 91720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.160 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 42.830 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.004 0.136 11548 Z= 0.256 Angle : 0.695 13.149 15914 Z= 0.372 Chirality : 0.048 0.530 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.012 137.923 4432 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1250 helix: 1.67 (0.20), residues: 697 sheet: 0.70 (0.54), residues: 93 loop : -0.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 PHE 0.012 0.001 PHE A 886 TYR 0.014 0.001 TYR B 161 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.074 Fit side-chains REVERT: A 467 GLU cc_start: 0.6632 (tp30) cc_final: 0.6321 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2429 time to fit residues: 56.1694 Evaluate side-chains 138 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11548 Z= 0.206 Angle : 0.563 8.491 15914 Z= 0.298 Chirality : 0.040 0.192 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.240 109.283 2047 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.85 % Allowed : 5.59 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1250 helix: 1.71 (0.20), residues: 696 sheet: 0.72 (0.52), residues: 103 loop : -0.98 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1110 HIS 0.007 0.001 HIS A1057 PHE 0.011 0.001 PHE B 229 TYR 0.017 0.002 TYR A1229 ARG 0.003 0.000 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.222 Fit side-chains REVERT: B 116 ARG cc_start: 0.6831 (mmm-85) cc_final: 0.6544 (mmm-85) REVERT: B 168 MET cc_start: 0.7534 (mmm) cc_final: 0.7260 (mmm) REVERT: B 267 MET cc_start: 0.7840 (mmm) cc_final: 0.7637 (mmm) REVERT: A 461 MET cc_start: 0.8701 (tmm) cc_final: 0.8053 (ttt) REVERT: A 467 GLU cc_start: 0.6642 (tp30) cc_final: 0.6380 (tp30) REVERT: A 533 ARG cc_start: 0.7379 (ttt180) cc_final: 0.7122 (tpt-90) outliers start: 9 outliers final: 6 residues processed: 149 average time/residue: 0.2632 time to fit residues: 55.1538 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A1032 GLN A1231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11548 Z= 0.201 Angle : 0.544 8.488 15914 Z= 0.287 Chirality : 0.039 0.164 1762 Planarity : 0.004 0.041 1828 Dihedral : 18.292 108.665 2047 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.04 % Allowed : 6.72 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1250 helix: 1.72 (0.20), residues: 693 sheet: 0.79 (0.53), residues: 103 loop : -1.01 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1110 HIS 0.006 0.001 HIS A1057 PHE 0.011 0.001 PHE B 229 TYR 0.012 0.001 TYR A 496 ARG 0.002 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.270 Fit side-chains REVERT: A 461 MET cc_start: 0.8679 (tmm) cc_final: 0.8100 (ttt) REVERT: A 518 LYS cc_start: 0.7351 (mttt) cc_final: 0.7125 (mmtp) REVERT: A 1105 MET cc_start: 0.8211 (mmm) cc_final: 0.7865 (mmp) outliers start: 11 outliers final: 9 residues processed: 145 average time/residue: 0.2550 time to fit residues: 53.0165 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.1980 chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11548 Z= 0.204 Angle : 0.540 8.595 15914 Z= 0.286 Chirality : 0.039 0.153 1762 Planarity : 0.004 0.055 1828 Dihedral : 18.367 108.196 2047 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.95 % Allowed : 8.52 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1250 helix: 1.72 (0.20), residues: 691 sheet: 0.84 (0.53), residues: 103 loop : -1.05 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 PHE 0.009 0.001 PHE B 318 TYR 0.012 0.001 TYR A 496 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.147 Fit side-chains REVERT: B 267 MET cc_start: 0.8046 (mmm) cc_final: 0.7738 (mmm) REVERT: A 461 MET cc_start: 0.8693 (tmm) cc_final: 0.8308 (ttt) REVERT: A 518 LYS cc_start: 0.7362 (mttt) cc_final: 0.7061 (mmtp) REVERT: A 875 PHE cc_start: 0.8336 (m-80) cc_final: 0.8079 (m-10) REVERT: A 926 GLU cc_start: 0.6916 (tt0) cc_final: 0.6706 (tt0) REVERT: A 1105 MET cc_start: 0.8213 (mmm) cc_final: 0.7867 (mmp) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.2509 time to fit residues: 51.9461 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11548 Z= 0.288 Angle : 0.590 9.122 15914 Z= 0.312 Chirality : 0.041 0.160 1762 Planarity : 0.005 0.045 1828 Dihedral : 18.660 109.179 2047 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 1.23 % Allowed : 9.85 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1250 helix: 1.45 (0.20), residues: 690 sheet: 0.68 (0.53), residues: 103 loop : -1.18 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 455 HIS 0.007 0.001 HIS A 943 PHE 0.012 0.001 PHE B 229 TYR 0.014 0.002 TYR A 496 ARG 0.004 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.267 Fit side-chains REVERT: B 116 ARG cc_start: 0.6810 (mmm-85) cc_final: 0.6341 (mmm-85) REVERT: A 461 MET cc_start: 0.8813 (tmm) cc_final: 0.8394 (ttt) REVERT: A 518 LYS cc_start: 0.7576 (mttt) cc_final: 0.7290 (mmtp) REVERT: A 533 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7247 (tpt-90) REVERT: A 875 PHE cc_start: 0.8374 (m-80) cc_final: 0.8116 (m-10) outliers start: 13 outliers final: 11 residues processed: 146 average time/residue: 0.2586 time to fit residues: 53.5924 Evaluate side-chains 148 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 40.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11548 Z= 0.188 Angle : 0.525 8.628 15914 Z= 0.279 Chirality : 0.039 0.143 1762 Planarity : 0.004 0.041 1828 Dihedral : 18.487 108.461 2047 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 1.14 % Allowed : 10.98 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1250 helix: 1.65 (0.20), residues: 689 sheet: 0.93 (0.53), residues: 101 loop : -1.12 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 PHE 0.010 0.001 PHE A 826 TYR 0.014 0.001 TYR A1229 ARG 0.004 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.148 Fit side-chains REVERT: B 42 TYR cc_start: 0.8269 (m-80) cc_final: 0.8022 (m-80) REVERT: B 119 VAL cc_start: 0.7980 (p) cc_final: 0.7646 (t) REVERT: A 461 MET cc_start: 0.8761 (tmm) cc_final: 0.8384 (ttt) REVERT: A 518 LYS cc_start: 0.7534 (mttt) cc_final: 0.7209 (mmtp) REVERT: A 533 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7241 (tpt-90) REVERT: A 891 LEU cc_start: 0.8828 (tt) cc_final: 0.8412 (mt) outliers start: 12 outliers final: 9 residues processed: 141 average time/residue: 0.2696 time to fit residues: 54.0815 Evaluate side-chains 146 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 0.0170 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11548 Z= 0.155 Angle : 0.503 8.462 15914 Z= 0.269 Chirality : 0.038 0.140 1762 Planarity : 0.004 0.037 1828 Dihedral : 18.372 107.317 2047 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 0.76 % Allowed : 12.41 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1250 helix: 1.77 (0.20), residues: 690 sheet: 1.02 (0.53), residues: 101 loop : -1.03 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 455 HIS 0.007 0.001 HIS A1057 PHE 0.011 0.001 PHE A 826 TYR 0.013 0.001 TYR B 161 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.160 Fit side-chains REVERT: B 119 VAL cc_start: 0.7976 (p) cc_final: 0.7652 (t) REVERT: A 461 MET cc_start: 0.8713 (tmm) cc_final: 0.8386 (ttt) REVERT: A 891 LEU cc_start: 0.8784 (tt) cc_final: 0.8370 (mt) outliers start: 8 outliers final: 7 residues processed: 139 average time/residue: 0.2564 time to fit residues: 50.7108 Evaluate side-chains 137 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 GLN A 981 HIS A1231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11548 Z= 0.296 Angle : 0.576 9.038 15914 Z= 0.306 Chirality : 0.041 0.149 1762 Planarity : 0.005 0.045 1828 Dihedral : 18.561 108.326 2047 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1250 helix: 1.48 (0.20), residues: 689 sheet: 0.85 (0.52), residues: 101 loop : -1.23 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 682 HIS 0.007 0.001 HIS A 943 PHE 0.010 0.001 PHE B 229 TYR 0.013 0.002 TYR A 496 ARG 0.003 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.241 Fit side-chains REVERT: B 42 TYR cc_start: 0.8277 (m-80) cc_final: 0.8075 (m-80) REVERT: A 461 MET cc_start: 0.8810 (tmm) cc_final: 0.8429 (ttt) REVERT: A 891 LEU cc_start: 0.8764 (tt) cc_final: 0.8353 (mt) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.2554 time to fit residues: 51.7021 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 119 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A 966 GLN A 981 HIS A1231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11548 Z= 0.290 Angle : 0.578 9.007 15914 Z= 0.307 Chirality : 0.041 0.150 1762 Planarity : 0.005 0.047 1828 Dihedral : 18.552 108.846 2047 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 1.33 % Allowed : 12.88 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1250 helix: 1.42 (0.20), residues: 684 sheet: 0.66 (0.53), residues: 95 loop : -1.25 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 24 HIS 0.008 0.001 HIS A 943 PHE 0.009 0.001 PHE A 404 TYR 0.013 0.002 TYR A 496 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: B 42 TYR cc_start: 0.8273 (m-80) cc_final: 0.7969 (m-80) REVERT: B 116 ARG cc_start: 0.6726 (mmm-85) cc_final: 0.6187 (mmm-85) REVERT: B 267 MET cc_start: 0.8117 (mmm) cc_final: 0.7673 (mmm) REVERT: A 461 MET cc_start: 0.8824 (tmm) cc_final: 0.8435 (ttt) REVERT: A 891 LEU cc_start: 0.8647 (tt) cc_final: 0.8296 (mt) outliers start: 14 outliers final: 13 residues processed: 144 average time/residue: 0.2654 time to fit residues: 53.7434 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 0.0970 chunk 109 optimal weight: 9.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 GLN A 981 HIS A1231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11548 Z= 0.181 Angle : 0.519 8.561 15914 Z= 0.277 Chirality : 0.038 0.152 1762 Planarity : 0.004 0.047 1828 Dihedral : 18.358 107.624 2047 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.14 % Allowed : 13.35 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1250 helix: 1.63 (0.20), residues: 687 sheet: 0.82 (0.54), residues: 95 loop : -1.12 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 24 HIS 0.006 0.001 HIS A1057 PHE 0.012 0.001 PHE A 826 TYR 0.011 0.001 TYR A 496 ARG 0.003 0.000 ARG A1220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 461 MET cc_start: 0.8769 (tmm) cc_final: 0.8422 (ttt) REVERT: A 891 LEU cc_start: 0.8614 (tt) cc_final: 0.8281 (mt) outliers start: 12 outliers final: 11 residues processed: 133 average time/residue: 0.2582 time to fit residues: 48.8241 Evaluate side-chains 140 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 chunk 12 optimal weight: 0.0270 chunk 18 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A 966 GLN A 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.164064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.130829 restraints weight = 26775.813| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.62 r_work: 0.3156 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 11548 Z= 0.281 Angle : 0.818 59.174 15914 Z= 0.481 Chirality : 0.046 1.117 1762 Planarity : 0.005 0.088 1828 Dihedral : 18.373 107.621 2047 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.95 % Allowed : 13.64 % Favored : 85.42 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.86 (0.24), residues: 1250 helix: 1.65 (0.20), residues: 687 sheet: 0.77 (0.54), residues: 95 loop : -1.12 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 24 HIS 0.006 0.001 HIS A1057 PHE 0.012 0.001 PHE A 826 TYR 0.011 0.001 TYR A 496 ARG 0.002 0.000 ARG A1220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.67 seconds wall clock time: 42 minutes 3.28 seconds (2523.28 seconds total)