Starting phenix.real_space_refine on Tue May 7 09:37:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4b_18884/05_2024/8r4b_18884_neut_updated.pdb" } resolution = 3.88 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= 0.002 sd= 0.063 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 3 5.49 5 S 24 5.16 5 C 4806 2.51 5 N 1277 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 504": "OD1" <-> "OD2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 7600 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 5956 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain breaks: 8 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 769 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 843 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.67, per 1000 atoms: 0.61 Number of scatterers: 7600 At special positions: 0 Unit cell: (70.97, 80.03, 182.71, 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 24 16.00 P 3 15.00 O 1490 8.00 N 1277 7.00 C 4806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 11 sheets defined 19.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.736A pdb=" N ILE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.522A pdb=" N SER A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 427 through 438 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 630 through 643 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.551A pdb=" N THR A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 705 " --> pdb=" O VAL A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 810 through 813 No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.128A pdb=" N GLU A 67 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET A 89 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET A 111 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU A 133 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A 155 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 177 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU A 221 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU A 243 " --> pdb=" O LEU A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.316A pdb=" N LYS A 287 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU A 309 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR A 331 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU A 353 " --> pdb=" O LEU A 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 396 through 398 Processing sheet with id= D, first strand: chain 'A' and resid 563 through 568 removed outlier: 8.611A pdb=" N VAL A 535 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 454 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N MET A 537 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS A 456 " --> pdb=" O MET A 537 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 539 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 458 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 510 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 455 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS A 512 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 457 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP A 514 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 799 through 802 Processing sheet with id= F, first strand: chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N LYS A 844 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 17 through 23 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.832A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 114 through 116 removed outlier: 5.960A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 99 through 101 167 hydrogen bonds defined for protein. 450 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: 2.31 Time building geometry restraints manager: 3.22 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: 2494 1.34 - 1.46: 1166 1.46 - 1.57: 4028 1.57 - 1.69: 5 1.69 - 1.81: 38 Bond restraints: 7731 Sorted by residual: bond pdb=" N GLU A 769 " pdb=" CA GLU A 769 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.67e+00 bond pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta sigma weight residual 1.469 1.485 -0.016 1.28e-02 6.10e+03 1.57e+00 bond pdb=" C ALA B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.340 1.373 -0.033 2.76e-02 1.31e+03 1.46e+00 bond pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " ideal model delta sigma weight residual 1.540 1.556 -0.016 1.36e-02 5.41e+03 1.36e+00 ... (remaining 7726 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 178 106.17 - 113.13: 4310 113.13 - 120.09: 2573 120.09 - 127.06: 3405 127.06 - 134.02: 88 Bond angle restraints: 10554 Sorted by residual: angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 113.20 109.25 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CD1 ILE A 144 " ideal model delta sigma weight residual 113.80 121.50 -7.70 2.10e+00 2.27e-01 1.34e+01 angle pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 110.40 116.37 -5.97 1.70e+00 3.46e-01 1.23e+01 angle pdb=" CA GLN A 12 " pdb=" CB GLN A 12 " pdb=" CG GLN A 12 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" N ALA C 91 " pdb=" CA ALA C 91 " pdb=" C ALA C 91 " ideal model delta sigma weight residual 108.34 112.10 -3.76 1.31e+00 5.83e-01 8.24e+00 ... (remaining 10549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 4185 22.03 - 44.05: 394 44.05 - 66.08: 46 66.08 - 88.11: 12 88.11 - 110.14: 2 Dihedral angle restraints: 4639 sinusoidal: 1637 harmonic: 3002 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 167.81 -74.81 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 141.71 -48.71 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" O3B GSP A1201 " pdb=" O3A GSP A1201 " pdb=" PB GSP A1201 " pdb=" PA GSP A1201 " ideal model delta sinusoidal sigma weight residual 93.55 -156.31 -110.14 1 2.00e+01 2.50e-03 3.23e+01 ... (remaining 4636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 768 0.033 - 0.067: 354 0.067 - 0.100: 105 0.100 - 0.133: 40 0.133 - 0.167: 4 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CA ILE A 821 " pdb=" N ILE A 821 " pdb=" C ILE A 821 " pdb=" CB ILE A 821 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ILE A 408 " pdb=" N ILE A 408 " pdb=" C ILE A 408 " pdb=" CB ILE A 408 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE A 565 " pdb=" N ILE A 565 " pdb=" C ILE A 565 " pdb=" CB ILE A 565 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1268 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 413 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO A 414 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 189 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 803 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" CG ASP A 803 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 803 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 803 " -0.010 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 708 2.75 - 3.28: 7565 3.28 - 3.82: 12410 3.82 - 4.36: 14781 4.36 - 4.90: 24861 Nonbonded interactions: 60325 Sorted by model distance: nonbonded pdb=" OH TYR A 45 " pdb=" OD1 ASN C 32 " model vdw 2.206 2.440 nonbonded pdb=" O SER A 417 " pdb=" OH TYR A 433 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 154 " pdb=" OE1 GLU A 155 " model vdw 2.283 2.440 nonbonded pdb=" O SER A 352 " pdb=" OG1 THR A 374 " model vdw 2.285 2.440 nonbonded pdb=" N GLU A 686 " pdb=" OE1 GLU A 686 " model vdw 2.289 2.520 ... (remaining 60320 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.920 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7731 Z= 0.212 Angle : 0.686 7.697 10554 Z= 0.365 Chirality : 0.044 0.167 1271 Planarity : 0.005 0.047 1346 Dihedral : 16.622 110.136 2681 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.51 % Favored : 90.19 % Rotamer: Outliers : 0.52 % Allowed : 20.63 % Favored : 78.85 % 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: -2.78 (0.25), residues: 1009 helix: -1.10 (0.34), residues: 233 sheet: -1.20 (0.32), residues: 250 loop : -2.57 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.004 0.001 HIS A 549 PHE 0.014 0.001 PHE A 410 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7587 (tt0) REVERT: A 252 THR cc_start: 0.7969 (p) cc_final: 0.7747 (m) REVERT: A 275 ASP cc_start: 0.6974 (t0) cc_final: 0.6558 (t0) REVERT: A 323 LEU cc_start: 0.7940 (tp) cc_final: 0.7739 (mm) REVERT: A 351 LEU cc_start: 0.8182 (mt) cc_final: 0.7940 (mt) REVERT: A 402 PHE cc_start: 0.6348 (t80) cc_final: 0.6051 (t80) REVERT: A 409 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 427 LYS cc_start: 0.7390 (tmtt) cc_final: 0.6904 (tttp) REVERT: A 432 GLN cc_start: 0.8751 (mt0) cc_final: 0.8031 (mm-40) REVERT: A 706 TYR cc_start: 0.3964 (t80) cc_final: 0.2587 (t80) REVERT: A 715 LYS cc_start: 0.8547 (tttt) cc_final: 0.8291 (tptt) REVERT: A 753 GLN cc_start: 0.6659 (tt0) cc_final: 0.6411 (tt0) REVERT: B 86 MET cc_start: 0.7352 (mmm) cc_final: 0.6425 (mmp) REVERT: C 12 VAL cc_start: 0.7922 (t) cc_final: 0.7583 (p) REVERT: C 45 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6855 (mtt180) REVERT: C 56 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7201 (mtm180) REVERT: C 80 LEU cc_start: 0.8706 (tp) cc_final: 0.8222 (tp) REVERT: C 114 THR cc_start: 0.8573 (m) cc_final: 0.8340 (p) outliers start: 4 outliers final: 1 residues processed: 230 average time/residue: 0.1912 time to fit residues: 59.6000 Evaluate side-chains 188 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 577 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 578 ASN A 819 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7731 Z= 0.305 Angle : 0.695 10.163 10554 Z= 0.355 Chirality : 0.046 0.318 1271 Planarity : 0.005 0.042 1346 Dihedral : 7.815 107.708 1094 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.30 % Favored : 88.31 % Rotamer: Outliers : 5.74 % Allowed : 22.06 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.25), residues: 1009 helix: -1.10 (0.35), residues: 227 sheet: -1.20 (0.33), residues: 237 loop : -2.58 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 36 HIS 0.012 0.002 HIS A 449 PHE 0.021 0.002 PHE A 410 TYR 0.018 0.002 TYR C 94 ARG 0.005 0.001 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8197 (tp) cc_final: 0.7894 (tt) REVERT: A 147 LEU cc_start: 0.8877 (mp) cc_final: 0.8630 (mm) REVERT: A 275 ASP cc_start: 0.7000 (t0) cc_final: 0.6684 (t0) REVERT: A 338 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7660 (mm110) REVERT: A 378 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7208 (p) REVERT: A 402 PHE cc_start: 0.6342 (t80) cc_final: 0.5997 (t80) REVERT: A 409 THR cc_start: 0.8278 (p) cc_final: 0.7938 (p) REVERT: A 427 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6840 (tttp) REVERT: A 432 GLN cc_start: 0.8696 (mt0) cc_final: 0.8369 (mm-40) REVERT: A 574 ASN cc_start: 0.7741 (t0) cc_final: 0.7480 (t0) REVERT: A 696 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5087 (pt) REVERT: A 715 LYS cc_start: 0.8614 (tttt) cc_final: 0.8362 (tptt) REVERT: A 758 ASP cc_start: 0.7326 (m-30) cc_final: 0.6895 (m-30) REVERT: B 86 MET cc_start: 0.7220 (mmm) cc_final: 0.6735 (mmm) REVERT: C 45 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6624 (mtt180) REVERT: C 64 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8843 (pttt) REVERT: C 66 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6862 (mtp-110) REVERT: C 80 LEU cc_start: 0.8652 (tp) cc_final: 0.8342 (tp) REVERT: C 114 THR cc_start: 0.8312 (m) cc_final: 0.8059 (p) outliers start: 44 outliers final: 26 residues processed: 227 average time/residue: 0.1946 time to fit residues: 59.6426 Evaluate side-chains 219 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.0370 chunk 90 optimal weight: 0.9990 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 762 GLN A 819 HIS C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.209 Angle : 0.633 8.081 10554 Z= 0.318 Chirality : 0.044 0.245 1271 Planarity : 0.004 0.039 1346 Dihedral : 7.402 110.073 1093 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.92 % Favored : 90.68 % Rotamer: Outliers : 5.61 % Allowed : 23.37 % Favored : 71.02 % 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: -2.56 (0.26), residues: 1009 helix: -0.90 (0.36), residues: 222 sheet: -0.99 (0.34), residues: 238 loop : -2.44 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.007 0.001 HIS A 523 PHE 0.015 0.002 PHE A 410 TYR 0.012 0.001 TYR C 94 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.5881 (p0) cc_final: 0.5061 (p0) REVERT: A 254 ILE cc_start: 0.7243 (tp) cc_final: 0.7041 (tt) REVERT: A 275 ASP cc_start: 0.6976 (t0) cc_final: 0.6614 (t0) REVERT: A 282 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 338 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7518 (mm-40) REVERT: A 402 PHE cc_start: 0.6360 (t80) cc_final: 0.6024 (t80) REVERT: A 409 THR cc_start: 0.8126 (p) cc_final: 0.7819 (p) REVERT: A 427 LYS cc_start: 0.7233 (tmtt) cc_final: 0.6771 (tttp) REVERT: A 432 GLN cc_start: 0.8702 (mt0) cc_final: 0.8458 (mm-40) REVERT: A 556 GLU cc_start: 0.6947 (tp30) cc_final: 0.6572 (tp30) REVERT: A 574 ASN cc_start: 0.7661 (t0) cc_final: 0.7415 (t0) REVERT: A 715 LYS cc_start: 0.8536 (tttt) cc_final: 0.8336 (tptt) REVERT: B 86 MET cc_start: 0.7253 (mmm) cc_final: 0.6316 (mmm) REVERT: C 45 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6540 (mtt180) REVERT: C 80 LEU cc_start: 0.8726 (tp) cc_final: 0.8350 (tp) REVERT: C 114 THR cc_start: 0.8294 (m) cc_final: 0.8056 (p) outliers start: 43 outliers final: 24 residues processed: 225 average time/residue: 0.1909 time to fit residues: 57.8676 Evaluate side-chains 209 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 overall best weight: 0.8092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS A 819 HIS C 96 ASN C 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7731 Z= 0.332 Angle : 0.703 8.370 10554 Z= 0.356 Chirality : 0.047 0.290 1271 Planarity : 0.005 0.045 1346 Dihedral : 7.971 117.567 1093 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.60 % Favored : 88.01 % Rotamer: Outliers : 7.44 % Allowed : 24.41 % Favored : 68.15 % 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: -2.68 (0.25), residues: 1009 helix: -1.15 (0.34), residues: 227 sheet: -0.96 (0.34), residues: 237 loop : -2.51 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 36 HIS 0.009 0.002 HIS A 523 PHE 0.017 0.002 PHE A 115 TYR 0.014 0.002 TYR C 37 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7674 (ptp90) cc_final: 0.6939 (ptt-90) REVERT: A 184 GLN cc_start: 0.7523 (mp10) cc_final: 0.7208 (mp10) REVERT: A 254 ILE cc_start: 0.7381 (tp) cc_final: 0.7063 (tp) REVERT: A 275 ASP cc_start: 0.7058 (t0) cc_final: 0.6634 (t0) REVERT: A 282 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 338 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7666 (mm-40) REVERT: A 378 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 402 PHE cc_start: 0.6305 (t80) cc_final: 0.5954 (t80) REVERT: A 409 THR cc_start: 0.8261 (p) cc_final: 0.8048 (p) REVERT: A 427 LYS cc_start: 0.7182 (tmtt) cc_final: 0.6686 (tttp) REVERT: A 432 GLN cc_start: 0.8701 (mt0) cc_final: 0.8490 (mm-40) REVERT: A 556 GLU cc_start: 0.6882 (tp30) cc_final: 0.6466 (tp30) REVERT: B 86 MET cc_start: 0.7245 (mmm) cc_final: 0.6251 (mmm) REVERT: C 80 LEU cc_start: 0.8611 (tp) cc_final: 0.8146 (tp) REVERT: C 86 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7976 (mttp) REVERT: C 114 THR cc_start: 0.8268 (m) cc_final: 0.8039 (p) outliers start: 57 outliers final: 47 residues processed: 230 average time/residue: 0.1859 time to fit residues: 58.5929 Evaluate side-chains 238 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.0030 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS C 96 ASN C 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7731 Z= 0.254 Angle : 0.657 7.888 10554 Z= 0.332 Chirality : 0.045 0.226 1271 Planarity : 0.005 0.058 1346 Dihedral : 7.750 119.578 1093 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.72 % Favored : 90.88 % Rotamer: Outliers : 7.31 % Allowed : 25.20 % Favored : 67.49 % 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: -2.58 (0.26), residues: 1009 helix: -1.09 (0.35), residues: 226 sheet: -0.87 (0.34), residues: 236 loop : -2.44 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 36 HIS 0.007 0.001 HIS A 456 PHE 0.016 0.002 PHE A 115 TYR 0.012 0.002 TYR B 60 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7604 (ptp90) cc_final: 0.6935 (ptt-90) REVERT: A 184 GLN cc_start: 0.7491 (mp10) cc_final: 0.7140 (mp10) REVERT: A 254 ILE cc_start: 0.7308 (tp) cc_final: 0.6981 (tp) REVERT: A 275 ASP cc_start: 0.7132 (t0) cc_final: 0.6746 (t0) REVERT: A 282 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 338 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7662 (mm-40) REVERT: A 378 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7579 (p) REVERT: A 402 PHE cc_start: 0.6307 (t80) cc_final: 0.5966 (t80) REVERT: A 427 LYS cc_start: 0.7151 (tmtt) cc_final: 0.6645 (tttp) REVERT: A 556 GLU cc_start: 0.6893 (tp30) cc_final: 0.6456 (tp30) REVERT: A 574 ASN cc_start: 0.7537 (t0) cc_final: 0.7319 (t0) REVERT: B 86 MET cc_start: 0.7253 (mmm) cc_final: 0.6220 (mmm) REVERT: C 80 LEU cc_start: 0.8639 (tp) cc_final: 0.8173 (tp) REVERT: C 114 THR cc_start: 0.8258 (m) cc_final: 0.8015 (p) outliers start: 56 outliers final: 44 residues processed: 229 average time/residue: 0.1766 time to fit residues: 55.3388 Evaluate side-chains 232 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7731 Z= 0.294 Angle : 0.690 7.973 10554 Z= 0.351 Chirality : 0.046 0.278 1271 Planarity : 0.005 0.041 1346 Dihedral : 7.873 122.560 1093 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.70 % Favored : 88.90 % Rotamer: Outliers : 8.09 % Allowed : 25.46 % Favored : 66.45 % 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: -2.63 (0.26), residues: 1009 helix: -1.26 (0.34), residues: 233 sheet: -0.88 (0.35), residues: 237 loop : -2.43 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 91 HIS 0.008 0.002 HIS A 456 PHE 0.015 0.002 PHE A 115 TYR 0.016 0.002 TYR A 536 ARG 0.005 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7589 (ptp90) cc_final: 0.6936 (ptt-90) REVERT: A 74 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: A 133 GLU cc_start: 0.8093 (tt0) cc_final: 0.7860 (tt0) REVERT: A 184 GLN cc_start: 0.7487 (mp10) cc_final: 0.7137 (mp10) REVERT: A 254 ILE cc_start: 0.7363 (tp) cc_final: 0.7055 (tp) REVERT: A 282 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 378 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8058 (m) REVERT: A 402 PHE cc_start: 0.6292 (t80) cc_final: 0.6085 (t80) REVERT: A 556 GLU cc_start: 0.6865 (tp30) cc_final: 0.6419 (tp30) REVERT: A 574 ASN cc_start: 0.7633 (t0) cc_final: 0.7401 (t0) REVERT: A 872 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5450 (mm) REVERT: B 86 MET cc_start: 0.7212 (mmm) cc_final: 0.6217 (mmm) REVERT: C 80 LEU cc_start: 0.8684 (tp) cc_final: 0.8242 (tp) REVERT: C 114 THR cc_start: 0.8257 (m) cc_final: 0.8009 (p) outliers start: 62 outliers final: 48 residues processed: 231 average time/residue: 0.1861 time to fit residues: 58.9058 Evaluate side-chains 244 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.209 Angle : 0.663 8.876 10554 Z= 0.330 Chirality : 0.044 0.221 1271 Planarity : 0.004 0.042 1346 Dihedral : 7.540 123.662 1093 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.42 % Favored : 91.18 % Rotamer: Outliers : 6.79 % Allowed : 27.28 % Favored : 65.93 % 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: -2.48 (0.26), residues: 1009 helix: -1.14 (0.35), residues: 234 sheet: -0.74 (0.35), residues: 239 loop : -2.36 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.005 0.001 HIS A 526 PHE 0.014 0.002 PHE A 115 TYR 0.011 0.001 TYR B 60 ARG 0.006 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 195 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7589 (ptp90) cc_final: 0.7319 (ptt180) REVERT: A 133 GLU cc_start: 0.8079 (tt0) cc_final: 0.7783 (tt0) REVERT: A 254 ILE cc_start: 0.7292 (tp) cc_final: 0.7062 (tp) REVERT: A 378 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (m) REVERT: A 427 LYS cc_start: 0.7272 (tptp) cc_final: 0.7035 (tptp) REVERT: A 547 ASN cc_start: 0.7062 (t0) cc_final: 0.6820 (p0) REVERT: A 556 GLU cc_start: 0.6895 (tp30) cc_final: 0.6450 (tp30) REVERT: A 574 ASN cc_start: 0.7605 (t0) cc_final: 0.7352 (t0) REVERT: A 872 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5672 (mm) REVERT: B 86 MET cc_start: 0.7308 (mmm) cc_final: 0.6432 (mmm) REVERT: C 80 LEU cc_start: 0.8649 (tp) cc_final: 0.8178 (tp) REVERT: C 114 THR cc_start: 0.8246 (m) cc_final: 0.7994 (p) outliers start: 52 outliers final: 38 residues processed: 224 average time/residue: 0.1794 time to fit residues: 55.2731 Evaluate side-chains 231 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS A 819 HIS ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN C 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7731 Z= 0.340 Angle : 0.736 8.305 10554 Z= 0.374 Chirality : 0.047 0.250 1271 Planarity : 0.005 0.044 1346 Dihedral : 8.024 127.088 1093 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.00 % Favored : 88.60 % Rotamer: Outliers : 7.83 % Allowed : 26.11 % Favored : 66.06 % 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: -2.66 (0.26), residues: 1009 helix: -1.40 (0.33), residues: 239 sheet: -0.84 (0.35), residues: 238 loop : -2.43 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 91 HIS 0.005 0.001 HIS A 526 PHE 0.016 0.002 PHE A 115 TYR 0.017 0.002 TYR A 536 ARG 0.006 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7629 (ptp90) cc_final: 0.7355 (ptt180) REVERT: A 74 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7967 (mm-40) REVERT: A 132 THR cc_start: 0.8162 (p) cc_final: 0.7767 (t) REVERT: A 254 ILE cc_start: 0.7352 (tp) cc_final: 0.7101 (tp) REVERT: A 323 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 378 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8028 (m) REVERT: A 427 LYS cc_start: 0.7236 (tptp) cc_final: 0.7012 (tptp) REVERT: A 432 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8482 (mm-40) REVERT: A 556 GLU cc_start: 0.6481 (tp30) cc_final: 0.6069 (tp30) REVERT: A 574 ASN cc_start: 0.7680 (t0) cc_final: 0.7405 (t0) REVERT: A 872 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5504 (mm) REVERT: B 86 MET cc_start: 0.7220 (mmm) cc_final: 0.6270 (mmm) REVERT: C 80 LEU cc_start: 0.8671 (tp) cc_final: 0.8238 (tp) REVERT: C 114 THR cc_start: 0.8328 (m) cc_final: 0.8028 (p) outliers start: 60 outliers final: 51 residues processed: 234 average time/residue: 0.1755 time to fit residues: 57.1471 Evaluate side-chains 252 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 197 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7731 Z= 0.250 Angle : 0.694 8.552 10554 Z= 0.352 Chirality : 0.045 0.235 1271 Planarity : 0.004 0.045 1346 Dihedral : 7.766 127.940 1093 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.62 % Favored : 90.98 % Rotamer: Outliers : 6.27 % Allowed : 28.59 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.26), residues: 1009 helix: -1.36 (0.33), residues: 240 sheet: -0.83 (0.35), residues: 238 loop : -2.42 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.008 0.001 HIS A 523 PHE 0.015 0.002 PHE A 115 TYR 0.044 0.002 TYR A 767 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7608 (ptp90) cc_final: 0.7406 (ptt180) REVERT: A 254 ILE cc_start: 0.7262 (tp) cc_final: 0.7061 (tp) REVERT: A 378 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (m) REVERT: A 427 LYS cc_start: 0.7259 (tptp) cc_final: 0.7037 (tptp) REVERT: A 547 ASN cc_start: 0.7348 (p0) cc_final: 0.7001 (t0) REVERT: A 556 GLU cc_start: 0.6519 (tp30) cc_final: 0.6152 (tp30) REVERT: A 574 ASN cc_start: 0.7648 (t0) cc_final: 0.7392 (t0) REVERT: A 872 ILE cc_start: 0.5664 (OUTLIER) cc_final: 0.5342 (mm) REVERT: B 86 MET cc_start: 0.7273 (mmm) cc_final: 0.6305 (mmm) REVERT: C 11 LEU cc_start: 0.8220 (tt) cc_final: 0.7967 (tt) REVERT: C 80 LEU cc_start: 0.8753 (tp) cc_final: 0.8273 (tp) REVERT: C 114 THR cc_start: 0.8309 (m) cc_final: 0.7975 (p) outliers start: 48 outliers final: 44 residues processed: 220 average time/residue: 0.1714 time to fit residues: 52.3343 Evaluate side-chains 236 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 92 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7731 Z= 0.271 Angle : 0.731 10.622 10554 Z= 0.367 Chirality : 0.046 0.241 1271 Planarity : 0.005 0.045 1346 Dihedral : 7.832 128.739 1093 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.32 % Favored : 90.29 % Rotamer: Outliers : 6.66 % Allowed : 28.33 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.26), residues: 1009 helix: -1.37 (0.33), residues: 234 sheet: -0.87 (0.35), residues: 240 loop : -2.40 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.009 0.002 HIS A 523 PHE 0.015 0.002 PHE A 883 TYR 0.038 0.002 TYR A 767 ARG 0.008 0.001 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7463 (ptp90) cc_final: 0.7058 (ptp-170) REVERT: A 74 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: A 378 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 427 LYS cc_start: 0.7281 (tptp) cc_final: 0.7054 (tptp) REVERT: A 547 ASN cc_start: 0.7444 (p0) cc_final: 0.6963 (t0) REVERT: A 556 GLU cc_start: 0.6449 (tp30) cc_final: 0.6133 (tp30) REVERT: A 574 ASN cc_start: 0.7648 (t0) cc_final: 0.7375 (t0) REVERT: A 872 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5365 (mm) REVERT: B 86 MET cc_start: 0.7232 (mmm) cc_final: 0.6267 (mmm) REVERT: C 11 LEU cc_start: 0.8239 (tt) cc_final: 0.7972 (tt) REVERT: C 80 LEU cc_start: 0.8742 (tp) cc_final: 0.8267 (tp) REVERT: C 114 THR cc_start: 0.8311 (m) cc_final: 0.8028 (t) outliers start: 51 outliers final: 44 residues processed: 224 average time/residue: 0.1698 time to fit residues: 52.7660 Evaluate side-chains 236 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.0170 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097523 restraints weight = 16105.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099353 restraints weight = 10650.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100692 restraints weight = 7861.163| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7731 Z= 0.227 Angle : 0.709 9.886 10554 Z= 0.357 Chirality : 0.045 0.226 1271 Planarity : 0.004 0.046 1346 Dihedral : 7.624 129.379 1093 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.62 % Favored : 90.98 % Rotamer: Outliers : 6.66 % Allowed : 28.72 % Favored : 64.62 % 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: -2.56 (0.26), residues: 1009 helix: -1.28 (0.34), residues: 241 sheet: -0.80 (0.35), residues: 241 loop : -2.39 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.007 0.001 HIS A 523 PHE 0.014 0.002 PHE A 115 TYR 0.032 0.002 TYR A 767 ARG 0.008 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.12 seconds wall clock time: 37 minutes 9.64 seconds (2229.64 seconds total)