Starting phenix.real_space_refine on Thu Feb 15 14:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/02_2024/7wvj_32853_updated.pdb" } resolution = 3.26 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= 0.001 sd= 0.058 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 90 5.49 5 S 34 5.16 5 C 7622 2.51 5 N 2108 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5281 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5281 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 917 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p_pyr': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1009 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p': 46} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Time building chain proxies: 6.72, per 1000 atoms: 0.54 Number of scatterers: 12488 At special positions: 0 Unit cell: (139.108, 135.854, 92.739, 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 34 16.00 P 90 15.00 O 2634 8.00 N 2108 7.00 C 7622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " 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: 5.29 Conformation dependent library (CDL) restraints added in 2.0 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 8.8% alpha, 7.6% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.270A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.762A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 671 through 674 No H-bonds generated for 'chain 'A' and resid 671 through 674' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.271A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.760A pdb=" N TRP B 273 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.304A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.058A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 326 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.454A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 639 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.259A pdb=" N TYR A 468 " --> pdb=" O GLN A 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.304A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.058A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 326 " --> pdb=" O PHE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.454A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU B 639 " --> pdb=" O LEU B 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.260A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 32 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3293 1.33 - 1.45: 2751 1.45 - 1.57: 6666 1.57 - 1.69: 180 1.69 - 1.81: 50 Bond restraints: 12940 Sorted by residual: bond pdb=" C2 I F 22 " pdb=" N3 I F 22 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2 I F 20 " pdb=" N3 I F 20 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" C2 I F 6 " pdb=" N3 I F 6 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C2 I F 36 " pdb=" N3 I F 36 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C2 I F 40 " pdb=" N3 I F 40 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 12935 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.15: 768 107.15 - 113.88: 7705 113.88 - 120.62: 4693 120.62 - 127.36: 4535 127.36 - 134.09: 293 Bond angle restraints: 17994 Sorted by residual: angle pdb=" C1' I F 37 " pdb=" N9 I F 37 " pdb=" C4 I F 37 " ideal model delta sigma weight residual 106.08 124.51 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C1' I F 46 " pdb=" N9 I F 46 " pdb=" C4 I F 46 " ideal model delta sigma weight residual 106.08 124.44 -18.36 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C1' I F 4 " pdb=" N9 I F 4 " pdb=" C4 I F 4 " ideal model delta sigma weight residual 106.08 124.37 -18.29 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C1' I F 43 " pdb=" N9 I F 43 " pdb=" C4 I F 43 " ideal model delta sigma weight residual 106.08 124.02 -17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" C1' I F 42 " pdb=" N9 I F 42 " pdb=" C4 I F 42 " ideal model delta sigma weight residual 106.08 124.00 -17.92 3.00e+00 1.11e-01 3.57e+01 ... (remaining 17989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6739 17.98 - 35.96: 552 35.96 - 53.95: 230 53.95 - 71.93: 126 71.93 - 89.91: 139 Dihedral angle restraints: 7786 sinusoidal: 3910 harmonic: 3876 Sorted by residual: dihedral pdb=" CA GLU B 626 " pdb=" C GLU B 626 " pdb=" N LYS B 627 " pdb=" CA LYS B 627 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU A 626 " pdb=" C GLU A 626 " pdb=" N LYS A 627 " pdb=" CA LYS A 627 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB LYS B 547 " pdb=" CG LYS B 547 " pdb=" CD LYS B 547 " pdb=" CE LYS B 547 " ideal model delta sinusoidal sigma weight residual -180.00 -122.13 -57.87 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1626 0.055 - 0.110: 276 0.110 - 0.165: 27 0.165 - 0.220: 0 0.220 - 0.275: 2 Chirality restraints: 1931 Sorted by residual: chirality pdb=" CB ILE A 668 " pdb=" CA ILE A 668 " pdb=" CG1 ILE A 668 " pdb=" CG2 ILE A 668 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE B 668 " pdb=" CA ILE B 668 " pdb=" CG1 ILE B 668 " pdb=" CG2 ILE B 668 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 521 " pdb=" N ILE A 521 " pdb=" C ILE A 521 " pdb=" CB ILE A 521 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1928 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 20 " -0.211 2.00e-02 2.50e+03 6.11e-01 8.39e+03 pdb=" C2' I F 20 " 0.179 2.00e-02 2.50e+03 pdb=" C3' I F 20 " 0.596 2.00e-02 2.50e+03 pdb=" C4' I F 20 " -0.445 2.00e-02 2.50e+03 pdb=" C5' I F 20 " -0.063 2.00e-02 2.50e+03 pdb=" N9 I F 20 " 0.945 2.00e-02 2.50e+03 pdb=" O2' I F 20 " -0.982 2.00e-02 2.50e+03 pdb=" O3' I F 20 " 0.648 2.00e-02 2.50e+03 pdb=" O4' I F 20 " -0.667 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 23 " -0.215 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C2' I F 23 " 0.192 2.00e-02 2.50e+03 pdb=" C3' I F 23 " 0.592 2.00e-02 2.50e+03 pdb=" C4' I F 23 " -0.446 2.00e-02 2.50e+03 pdb=" C5' I F 23 " -0.050 2.00e-02 2.50e+03 pdb=" N9 I F 23 " 0.926 2.00e-02 2.50e+03 pdb=" O2' I F 23 " -0.954 2.00e-02 2.50e+03 pdb=" O3' I F 23 " 0.622 2.00e-02 2.50e+03 pdb=" O4' I F 23 " -0.668 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 24 " 0.221 2.00e-02 2.50e+03 5.95e-01 7.96e+03 pdb=" C2' I F 24 " -0.186 2.00e-02 2.50e+03 pdb=" C3' I F 24 " -0.596 2.00e-02 2.50e+03 pdb=" C4' I F 24 " 0.436 2.00e-02 2.50e+03 pdb=" C5' I F 24 " 0.055 2.00e-02 2.50e+03 pdb=" N9 I F 24 " -0.912 2.00e-02 2.50e+03 pdb=" O2' I F 24 " 0.961 2.00e-02 2.50e+03 pdb=" O3' I F 24 " -0.621 2.00e-02 2.50e+03 pdb=" O4' I F 24 " 0.642 2.00e-02 2.50e+03 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3313 2.80 - 3.33: 11037 3.33 - 3.85: 21984 3.85 - 4.38: 25962 4.38 - 4.90: 41516 Nonbonded interactions: 103812 Sorted by model distance: nonbonded pdb=" O PRO B 46 " pdb=" OH TYR B 74 " model vdw 2.279 2.440 nonbonded pdb=" O PRO A 46 " pdb=" OH TYR A 74 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP B 648 " pdb=" OG SER B 653 " model vdw 2.295 2.440 nonbonded pdb=" O ASP B 648 " pdb=" OG SER B 653 " model vdw 2.297 2.440 nonbonded pdb=" O ASP A 648 " pdb=" OG SER A 653 " model vdw 2.297 2.440 ... (remaining 103807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 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: 3.170 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: 11.640 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.400 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.015 0.147 12940 Z= 0.777 Angle : 1.520 18.431 17994 Z= 0.552 Chirality : 0.041 0.275 1931 Planarity : 0.087 0.611 2022 Dihedral : 21.290 89.909 5238 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.16 % Allowed : 0.82 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.88 (0.24), residues: 1314 helix: -2.52 (0.40), residues: 122 sheet: -2.10 (0.40), residues: 208 loop : -0.89 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 353 HIS 0.004 0.001 HIS B 684 PHE 0.012 0.001 PHE A 303 TYR 0.016 0.002 TYR A 468 ARG 0.005 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.248 Fit side-chains REVERT: A 100 MET cc_start: 0.7147 (pmm) cc_final: 0.6676 (pmm) REVERT: B 309 ASN cc_start: 0.6687 (t0) cc_final: 0.6381 (t0) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.1916 time to fit residues: 40.9159 Evaluate side-chains 94 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 648 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 96 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 565 HIS B 39 HIS B 96 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN B 359 HIS B 563 HIS B 565 HIS ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12940 Z= 0.354 Angle : 1.945 17.686 17994 Z= 1.213 Chirality : 0.044 0.188 1931 Planarity : 0.017 0.127 2022 Dihedral : 24.535 97.574 2654 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.71 % Allowed : 7.83 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.01 (0.24), residues: 1314 helix: -2.05 (0.44), residues: 118 sheet: -2.00 (0.41), residues: 206 loop : -1.14 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 429 HIS 0.008 0.001 HIS B 156 PHE 0.019 0.002 PHE A 303 TYR 0.016 0.002 TYR B 468 ARG 0.004 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.433 Fit side-chains REVERT: A 301 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: A 305 LEU cc_start: 0.8172 (mt) cc_final: 0.7944 (mt) REVERT: A 309 ASN cc_start: 0.6718 (t0) cc_final: 0.6447 (t0) REVERT: B 309 ASN cc_start: 0.6708 (t0) cc_final: 0.6432 (t0) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.1800 time to fit residues: 31.3113 Evaluate side-chains 94 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 273 TRP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12940 Z= 0.295 Angle : 1.827 15.762 17994 Z= 1.155 Chirality : 0.043 0.165 1931 Planarity : 0.018 0.124 2022 Dihedral : 25.246 97.589 2652 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.79 % Allowed : 11.09 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.07 (0.24), residues: 1314 helix: -2.14 (0.43), residues: 118 sheet: -2.13 (0.40), residues: 206 loop : -1.15 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 429 HIS 0.008 0.001 HIS B 156 PHE 0.015 0.001 PHE B 303 TYR 0.018 0.002 TYR B 468 ARG 0.004 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.311 Fit side-chains REVERT: B 302 TYR cc_start: 0.8147 (m-80) cc_final: 0.7842 (m-80) REVERT: B 309 ASN cc_start: 0.6430 (t0) cc_final: 0.6155 (t0) outliers start: 22 outliers final: 19 residues processed: 105 average time/residue: 0.1813 time to fit residues: 31.8262 Evaluate side-chains 99 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 0.1980 chunk 115 optimal weight: 0.0770 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 overall best weight: 2.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN B 39 HIS B 148 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12940 Z= 0.386 Angle : 1.812 15.742 17994 Z= 1.151 Chirality : 0.045 0.170 1931 Planarity : 0.018 0.126 2022 Dihedral : 25.344 99.964 2650 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.53 % Allowed : 13.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.36 (0.24), residues: 1314 helix: -2.28 (0.43), residues: 118 sheet: -2.53 (0.39), residues: 188 loop : -1.35 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 429 HIS 0.006 0.001 HIS B 684 PHE 0.018 0.002 PHE B 557 TYR 0.018 0.002 TYR B 468 ARG 0.005 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 1.296 Fit side-chains REVERT: B 243 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8051 (mt) REVERT: B 302 TYR cc_start: 0.8213 (m-80) cc_final: 0.8003 (m-80) REVERT: B 309 ASN cc_start: 0.6686 (t0) cc_final: 0.6425 (t0) outliers start: 31 outliers final: 25 residues processed: 110 average time/residue: 0.1713 time to fit residues: 31.6673 Evaluate side-chains 102 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 0.0870 chunk 96 optimal weight: 0.0170 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN B 503 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12940 Z= 0.222 Angle : 1.749 14.731 17994 Z= 1.131 Chirality : 0.041 0.148 1931 Planarity : 0.018 0.120 2022 Dihedral : 25.384 97.880 2650 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.28 % Allowed : 14.52 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.18 (0.24), residues: 1314 helix: -1.95 (0.47), residues: 106 sheet: -2.46 (0.40), residues: 184 loop : -1.26 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 429 HIS 0.004 0.001 HIS B 684 PHE 0.012 0.001 PHE B 349 TYR 0.016 0.001 TYR B 468 ARG 0.001 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.531 Fit side-chains REVERT: A 86 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 309 ASN cc_start: 0.6392 (t0) cc_final: 0.6137 (t0) outliers start: 28 outliers final: 19 residues processed: 111 average time/residue: 0.1895 time to fit residues: 34.3369 Evaluate side-chains 98 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 638 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.0870 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12940 Z= 0.255 Angle : 1.744 14.708 17994 Z= 1.128 Chirality : 0.042 0.145 1931 Planarity : 0.018 0.122 2022 Dihedral : 25.520 93.393 2650 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.77 % Allowed : 15.09 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.21 (0.24), residues: 1314 helix: -2.07 (0.44), residues: 118 sheet: -2.57 (0.39), residues: 188 loop : -1.23 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 429 HIS 0.005 0.001 HIS B 684 PHE 0.017 0.001 PHE B 349 TYR 0.020 0.001 TYR B 468 ARG 0.004 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 1.322 Fit side-chains REVERT: A 86 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8189 (p) REVERT: B 309 ASN cc_start: 0.6559 (t0) cc_final: 0.6320 (t0) outliers start: 34 outliers final: 26 residues processed: 109 average time/residue: 0.1767 time to fit residues: 32.6394 Evaluate side-chains 105 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 638 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12940 Z= 0.288 Angle : 1.748 14.623 17994 Z= 1.129 Chirality : 0.043 0.177 1931 Planarity : 0.018 0.123 2022 Dihedral : 25.536 89.672 2650 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.02 % Allowed : 15.66 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.27 (0.24), residues: 1314 helix: -1.97 (0.47), residues: 106 sheet: -2.55 (0.39), residues: 184 loop : -1.33 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 429 HIS 0.005 0.001 HIS B 684 PHE 0.016 0.001 PHE B 349 TYR 0.017 0.002 TYR B 468 ARG 0.004 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 82 time to evaluate : 1.320 Fit side-chains REVERT: A 86 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 243 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 309 ASN cc_start: 0.6585 (t0) cc_final: 0.6383 (t0) outliers start: 37 outliers final: 29 residues processed: 109 average time/residue: 0.1803 time to fit residues: 32.3222 Evaluate side-chains 109 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 651 CYS Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 0.0020 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN B 541 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12940 Z= 0.183 Angle : 1.727 14.847 17994 Z= 1.124 Chirality : 0.040 0.209 1931 Planarity : 0.017 0.121 2022 Dihedral : 25.553 89.809 2650 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.71 % Allowed : 16.97 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.18 (0.24), residues: 1314 helix: -1.81 (0.45), residues: 118 sheet: -2.42 (0.40), residues: 180 loop : -1.29 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 429 HIS 0.003 0.001 HIS B 108 PHE 0.012 0.001 PHE A 502 TYR 0.017 0.001 TYR B 468 ARG 0.002 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.269 Fit side-chains REVERT: A 86 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 243 LEU cc_start: 0.8208 (tt) cc_final: 0.7952 (mt) REVERT: A 302 TYR cc_start: 0.8190 (m-80) cc_final: 0.7931 (m-80) REVERT: A 486 MET cc_start: 0.6345 (mmm) cc_final: 0.6123 (tpp) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.1911 time to fit residues: 31.8774 Evaluate side-chains 96 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN B 85 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12940 Z= 0.244 Angle : 1.734 14.711 17994 Z= 1.125 Chirality : 0.042 0.179 1931 Planarity : 0.018 0.123 2022 Dihedral : 25.599 89.897 2650 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.96 % Allowed : 17.21 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.26 (0.24), residues: 1314 helix: -2.04 (0.41), residues: 130 sheet: -2.62 (0.39), residues: 184 loop : -1.26 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 429 HIS 0.005 0.001 HIS B 684 PHE 0.012 0.001 PHE B 349 TYR 0.011 0.001 TYR B 326 ARG 0.003 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.239 Fit side-chains REVERT: A 86 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 243 LEU cc_start: 0.8234 (tt) cc_final: 0.7982 (mt) REVERT: A 302 TYR cc_start: 0.8265 (m-80) cc_final: 0.7973 (m-80) outliers start: 24 outliers final: 20 residues processed: 100 average time/residue: 0.1559 time to fit residues: 26.3706 Evaluate side-chains 101 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 651 CYS Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12940 Z= 0.283 Angle : 1.743 14.629 17994 Z= 1.127 Chirality : 0.043 0.167 1931 Planarity : 0.018 0.124 2022 Dihedral : 25.556 89.930 2650 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.28 % Allowed : 16.97 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.35 (0.24), residues: 1314 helix: -2.05 (0.44), residues: 118 sheet: -2.61 (0.40), residues: 180 loop : -1.38 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 429 HIS 0.005 0.001 HIS B 684 PHE 0.013 0.001 PHE B 349 TYR 0.012 0.001 TYR B 326 ARG 0.003 0.000 ARG B 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.271 Fit side-chains REVERT: A 86 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 243 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 302 TYR cc_start: 0.8293 (m-80) cc_final: 0.7959 (m-80) outliers start: 28 outliers final: 25 residues processed: 105 average time/residue: 0.1802 time to fit residues: 31.5296 Evaluate side-chains 104 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 651 CYS Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.167795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.133245 restraints weight = 23876.121| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.81 r_work: 0.3828 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12940 Z= 0.216 Angle : 1.729 14.628 17994 Z= 1.124 Chirality : 0.041 0.160 1931 Planarity : 0.018 0.121 2022 Dihedral : 25.491 89.764 2650 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.79 % Allowed : 17.54 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1314 helix: -2.01 (0.44), residues: 118 sheet: -2.58 (0.40), residues: 180 loop : -1.33 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 429 HIS 0.004 0.001 HIS B 684 PHE 0.012 0.001 PHE B 502 TYR 0.010 0.001 TYR B 462 ARG 0.002 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2586.30 seconds wall clock time: 48 minutes 30.86 seconds (2910.86 seconds total)