Starting phenix.real_space_refine on Sat Dec 9 22:10:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_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_32853/12_2023/7wvj_32853_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_32853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvj_32853/12_2023/7wvj_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-1.21rc1-5172/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: 6.82, per 1000 atoms: 0.55 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: 5.38 Conformation dependent library (CDL) restraints added in 2.1 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: 5.14 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: 3.88 Time building geometry restraints manager: 5.74 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: 3.300 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: 10.400 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 38.210 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- 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 : 1.327 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.1924 time to fit residues: 41.0523 Evaluate side-chains 93 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1137 time to fit residues: 2.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 HIS B 563 HIS B 565 HIS ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2405 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= 0.353 Angle : 1.943 17.993 17994 Z= 1.210 Chirality : 0.044 0.185 1931 Planarity : 0.018 0.129 2022 Dihedral : 24.526 98.257 2650 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.55 % Allowed : 7.91 % Favored : 90.54 % 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 (0.43), 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 109 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.366 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.1864 time to fit residues: 31.3099 Evaluate side-chains 90 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.363 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1183 time to fit residues: 4.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12940 Z= 0.287 Angle : 1.833 15.593 17994 Z= 1.155 Chirality : 0.042 0.177 1931 Planarity : 0.018 0.123 2022 Dihedral : 25.231 97.632 2650 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.57 % Allowed : 11.66 % Favored : 87.77 % 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: -2.05 (0.24), residues: 1314 helix: -2.09 (0.43), residues: 118 sheet: -2.14 (0.40), 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 0.015 0.001 PHE B 303 TYR 0.018 0.002 TYR B 468 ARG 0.007 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 100 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.329 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 99 average time/residue: 0.1777 time to fit residues: 29.6471 Evaluate side-chains 88 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1126 time to fit residues: 3.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 0.0770 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 39 HIS B 148 ASN B 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12940 Z= 0.170 Angle : 1.751 15.079 17994 Z= 1.135 Chirality : 0.039 0.147 1931 Planarity : 0.017 0.120 2022 Dihedral : 25.244 100.480 2650 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.73 % Allowed : 12.81 % Favored : 86.46 % 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: -1.96 (0.24), residues: 1314 helix: -1.89 (0.45), residues: 118 sheet: -2.17 (0.42), residues: 184 loop : -1.10 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 452 HIS 0.005 0.001 HIS B 156 PHE 0.010 0.001 PHE B 303 TYR 0.019 0.001 TYR B 468 ARG 0.002 0.000 ARG B 331 *********************** 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 105 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.339 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 0.2051 time to fit residues: 32.8595 Evaluate side-chains 88 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1413 time to fit residues: 2.6321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** 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 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN B 39 HIS ** B 148 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: 0.7149 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12940 Z= 0.432 Angle : 1.784 15.767 17994 Z= 1.140 Chirality : 0.046 0.196 1931 Planarity : 0.018 0.127 2022 Dihedral : 25.569 98.632 2650 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 1.79 % Allowed : 14.76 % Favored : 83.44 % 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: -2.42 (0.24), residues: 1314 helix: -2.25 (0.42), residues: 132 sheet: -2.67 (0.38), residues: 190 loop : -1.36 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.008 0.001 HIS B 684 PHE 0.021 0.002 PHE B 557 TYR 0.016 0.002 TYR A 326 ARG 0.005 0.001 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 107 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.402 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 0.1878 time to fit residues: 31.8125 Evaluate side-chains 85 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1128 time to fit residues: 4.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 0.0030 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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 503 GLN B 39 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN B 503 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12940 Z= 0.227 Angle : 1.741 14.613 17994 Z= 1.128 Chirality : 0.041 0.146 1931 Planarity : 0.018 0.121 2022 Dihedral : 25.494 95.922 2650 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.98 % Allowed : 15.66 % Favored : 83.36 % 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: -2.10 (0.24), residues: 1314 helix: -1.72 (0.49), residues: 106 sheet: -2.44 (0.40), residues: 180 loop : -1.23 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.004 0.001 HIS B 684 PHE 0.013 0.001 PHE B 349 TYR 0.009 0.001 TYR A 462 ARG 0.005 0.000 ARG A 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 103 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.357 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 99 average time/residue: 0.1971 time to fit residues: 32.1939 Evaluate side-chains 82 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1380 time to fit residues: 2.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 0.3980 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 85 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4235 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= 0.276 Angle : 1.746 14.758 17994 Z= 1.128 Chirality : 0.043 0.183 1931 Planarity : 0.018 0.123 2022 Dihedral : 25.579 92.161 2650 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.39 % Allowed : 16.15 % Favored : 82.46 % 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: -2.22 (0.24), residues: 1314 helix: -1.82 (0.48), residues: 106 sheet: -2.63 (0.40), residues: 184 loop : -1.28 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 429 HIS 0.005 0.001 HIS B 684 PHE 0.013 0.001 PHE B 557 TYR 0.011 0.002 TYR B 326 ARG 0.003 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 97 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.312 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 93 average time/residue: 0.1927 time to fit residues: 29.8385 Evaluate side-chains 84 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1185 time to fit residues: 3.3367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 12 optimal weight: 0.0060 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 0.0070 overall best weight: 1.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12940 Z= 0.211 Angle : 1.731 14.619 17994 Z= 1.125 Chirality : 0.041 0.165 1931 Planarity : 0.018 0.122 2022 Dihedral : 25.578 89.510 2650 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.82 % Allowed : 16.31 % Favored : 82.87 % 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: -2.17 (0.24), residues: 1314 helix: -1.77 (0.46), residues: 118 sheet: -2.47 (0.40), residues: 180 loop : -1.27 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 429 HIS 0.004 0.001 HIS B 684 PHE 0.012 0.001 PHE B 502 TYR 0.009 0.001 TYR A 462 ARG 0.003 0.000 ARG A 331 *********************** 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 95 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.302 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.2022 time to fit residues: 29.8132 Evaluate side-chains 84 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1370 time to fit residues: 2.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12940 Z= 0.238 Angle : 1.729 14.591 17994 Z= 1.124 Chirality : 0.041 0.145 1931 Planarity : 0.018 0.123 2022 Dihedral : 25.658 89.976 2650 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.49 % Allowed : 16.48 % Favored : 83.03 % 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: -2.31 (0.24), residues: 1314 helix: -1.96 (0.43), residues: 132 sheet: -2.57 (0.40), residues: 180 loop : -1.34 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 429 HIS 0.005 0.001 HIS B 684 PHE 0.013 0.001 PHE A 194 TYR 0.010 0.001 TYR A 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 91 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.987 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.1439 time to fit residues: 21.6128 Evaluate side-chains 83 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1110 time to fit residues: 2.5110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 88 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 365 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12940 Z= 0.305 Angle : 1.741 14.517 17994 Z= 1.127 Chirality : 0.044 0.164 1931 Planarity : 0.018 0.126 2022 Dihedral : 25.615 89.682 2650 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.24 % Allowed : 17.05 % Favored : 82.71 % 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: -2.40 (0.24), residues: 1314 helix: -1.93 (0.45), residues: 118 sheet: -2.80 (0.39), residues: 184 loop : -1.39 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 429 HIS 0.006 0.001 HIS B 684 PHE 0.014 0.001 PHE B 557 TYR 0.012 0.002 TYR B 383 ARG 0.004 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 89 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.298 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.1912 time to fit residues: 28.0248 Evaluate side-chains 80 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1106 time to fit residues: 1.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 0.0060 chunk 19 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** 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 = 0.4454 r_free = 0.4454 target = 0.168607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.134478 restraints weight = 23761.731| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.68 r_work: 0.3846 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12940 Z= 0.187 Angle : 1.716 14.734 17994 Z= 1.121 Chirality : 0.040 0.148 1931 Planarity : 0.017 0.121 2022 Dihedral : 25.594 89.916 2650 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.16 % Allowed : 17.29 % Favored : 82.54 % 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: -2.20 (0.24), residues: 1314 helix: -1.82 (0.45), residues: 118 sheet: -2.59 (0.40), residues: 180 loop : -1.27 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 353 HIS 0.003 0.001 HIS B 684 PHE 0.010 0.001 PHE B 502 TYR 0.011 0.001 TYR A 462 ARG 0.001 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.22 seconds wall clock time: 50 minutes 38.65 seconds (3038.65 seconds total)