Starting phenix.real_space_refine on Fri Mar 15 22:31:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/03_2024/7wv5_32846_updated.pdb" } resolution = 3.1 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= 0.068 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 7898 2.51 5 N 2144 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12958 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 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: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 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 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.18, per 1000 atoms: 0.55 Number of scatterers: 12958 At special positions: 0 Unit cell: (108.328, 168.601, 100.183, 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 2792 8.00 N 2144 7.00 C 7898 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=2.02 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=2.02 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " BMA H 3 " - " BMA H 4 " " BMA M 3 " - " BMA M 4 " NAG-ASN " NAG A 801 " - " ASN A 196 " " NAG A 802 " - " ASN A 398 " " NAG A 803 " - " ASN A 636 " " NAG A 804 " - " ASN A 662 " " NAG A 805 " - " ASN A 265 " " NAG B 801 " - " ASN B 196 " " NAG B 802 " - " ASN B 398 " " NAG B 803 " - " ASN B 636 " " NAG B 804 " - " ASN B 662 " " NAG B 805 " - " ASN B 265 " " NAG C 1 " - " ASN A 252 " " NAG D 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 291 " " NAG H 1 " - " ASN A 413 " " NAG I 1 " - " ASN A 507 " " NAG J 1 " - " ASN B 252 " " NAG K 1 " - " ASN B 275 " " NAG L 1 " - " ASN B 291 " " NAG M 1 " - " ASN B 413 " " NAG N 1 " - " ASN B 507 " Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 2.2 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: 26 helices and 8 sheets defined 9.7% alpha, 7.9% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.524A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.685A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.894A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.578A pdb=" N SER A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' 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 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' 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 68 through 71 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.525A pdb=" N LYS B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.685A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.894A pdb=" N TRP B 273 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 4.577A pdb=" N SER B 403 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' 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 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' 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: 6.410A pdb=" N VAL A 55 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 79 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 5.950A 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: 6.315A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.216A 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 383 through 385 removed outlier: 6.144A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.353A 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: 6.409A pdb=" N VAL B 55 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER B 79 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.667A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.950A 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: 6.315A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.216A 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 383 through 385 removed outlier: 6.143A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.569A 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: 6.353A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 34 hydrogen bonds defined for protein. 60 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: 4.18 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3786 1.34 - 1.46: 3332 1.46 - 1.58: 6062 1.58 - 1.70: 180 1.70 - 1.82: 50 Bond restraints: 13410 Sorted by residual: bond pdb=" C2 I F 21 " pdb=" N3 I F 21 " ideal model delta sigma weight residual 1.462 1.308 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" C2 I F 22 " pdb=" N3 I F 22 " ideal model delta sigma weight residual 1.462 1.310 0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C2 I F 19 " pdb=" N3 I F 19 " ideal model delta sigma weight residual 1.462 1.310 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C2 I F 18 " pdb=" N3 I F 18 " ideal model delta sigma weight residual 1.462 1.310 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C2 I F 29 " pdb=" N3 I F 29 " ideal model delta sigma weight residual 1.462 1.311 0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 13405 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 754 106.74 - 113.56: 8119 113.56 - 120.38: 4543 120.38 - 127.21: 4902 127.21 - 134.03: 306 Bond angle restraints: 18624 Sorted by residual: angle pdb=" C1' I F 22 " pdb=" N9 I F 22 " pdb=" C4 I F 22 " ideal model delta sigma weight residual 106.08 124.17 -18.09 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C1' I F 2 " pdb=" N9 I F 2 " pdb=" C4 I F 2 " ideal model delta sigma weight residual 106.08 124.17 -18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C1' I F 26 " pdb=" N9 I F 26 " pdb=" C4 I F 26 " ideal model delta sigma weight residual 106.08 124.13 -18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C1' I F 15 " pdb=" N9 I F 15 " pdb=" C4 I F 15 " ideal model delta sigma weight residual 106.08 124.04 -17.96 3.00e+00 1.11e-01 3.58e+01 angle pdb=" C1' I F 43 " pdb=" N9 I F 43 " pdb=" C4 I F 43 " ideal model delta sigma weight residual 106.08 124.00 -17.92 3.00e+00 1.11e-01 3.57e+01 ... (remaining 18619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 7745 21.86 - 43.73: 366 43.73 - 65.59: 205 65.59 - 87.46: 140 87.46 - 109.32: 48 Dihedral angle restraints: 8504 sinusoidal: 4628 harmonic: 3876 Sorted by residual: dihedral pdb=" O4 BMA M 4 " pdb=" C4 BMA M 4 " pdb=" C5 BMA M 4 " pdb=" O5 BMA M 4 " ideal model delta sinusoidal sigma weight residual 288.71 179.39 109.32 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA H 4 " pdb=" C4 BMA H 4 " pdb=" C5 BMA H 4 " pdb=" O5 BMA H 4 " ideal model delta sinusoidal sigma weight residual 288.71 179.40 109.31 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C3 BMA H 4 " pdb=" C4 BMA H 4 " pdb=" C5 BMA H 4 " pdb=" O5 BMA H 4 " ideal model delta sinusoidal sigma weight residual 47.62 -59.70 107.32 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1889 0.079 - 0.158: 199 0.158 - 0.237: 3 0.237 - 0.316: 4 0.316 - 0.395: 6 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 662 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C1 NAG B 804 " pdb=" ND2 ASN B 662 " pdb=" C2 NAG B 804 " pdb=" O5 NAG B 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG B 805 " pdb=" ND2 ASN B 265 " pdb=" C2 NAG B 805 " pdb=" O5 NAG B 805 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 2098 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 19 " -0.212 2.00e-02 2.50e+03 6.05e-01 8.24e+03 pdb=" C2' I F 19 " 0.182 2.00e-02 2.50e+03 pdb=" C3' I F 19 " 0.598 2.00e-02 2.50e+03 pdb=" C4' I F 19 " -0.442 2.00e-02 2.50e+03 pdb=" C5' I F 19 " -0.059 2.00e-02 2.50e+03 pdb=" N9 I F 19 " 0.927 2.00e-02 2.50e+03 pdb=" O2' I F 19 " -0.981 2.00e-02 2.50e+03 pdb=" O3' I F 19 " 0.640 2.00e-02 2.50e+03 pdb=" O4' I F 19 " -0.655 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 20 " -0.213 2.00e-02 2.50e+03 6.02e-01 8.15e+03 pdb=" C2' I F 20 " 0.186 2.00e-02 2.50e+03 pdb=" C3' I F 20 " 0.601 2.00e-02 2.50e+03 pdb=" C4' I F 20 " -0.440 2.00e-02 2.50e+03 pdb=" C5' I F 20 " -0.059 2.00e-02 2.50e+03 pdb=" N9 I F 20 " 0.922 2.00e-02 2.50e+03 pdb=" O2' I F 20 " -0.979 2.00e-02 2.50e+03 pdb=" O3' I F 20 " 0.630 2.00e-02 2.50e+03 pdb=" O4' I F 20 " -0.647 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 46 " -0.218 2.00e-02 2.50e+03 6.02e-01 8.15e+03 pdb=" C2' I F 46 " 0.185 2.00e-02 2.50e+03 pdb=" C3' I F 46 " 0.597 2.00e-02 2.50e+03 pdb=" C4' I F 46 " -0.440 2.00e-02 2.50e+03 pdb=" C5' I F 46 " -0.056 2.00e-02 2.50e+03 pdb=" N9 I F 46 " 0.930 2.00e-02 2.50e+03 pdb=" O2' I F 46 " -0.967 2.00e-02 2.50e+03 pdb=" O3' I F 46 " 0.627 2.00e-02 2.50e+03 pdb=" O4' I F 46 " -0.657 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3070 2.79 - 3.32: 11560 3.32 - 3.84: 22617 3.84 - 4.37: 27644 4.37 - 4.90: 43810 Nonbonded interactions: 108701 Sorted by model distance: nonbonded pdb=" OG SER B 115 " pdb=" OG1 THR B 118 " model vdw 2.260 2.440 nonbonded pdb=" OG SER A 115 " pdb=" OG1 THR A 118 " model vdw 2.261 2.440 nonbonded pdb=" O PRO A 46 " pdb=" OH TYR A 74 " model vdw 2.284 2.440 nonbonded pdb=" O PRO B 46 " pdb=" OH TYR B 74 " model vdw 2.284 2.440 nonbonded pdb=" O ASP B 47 " pdb=" NH1 ARG B 73 " model vdw 2.293 2.520 ... (remaining 108696 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'M' } 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: 8.070 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: 25.510 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 42.210 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.016 0.154 13410 Z= 1.018 Angle : 1.543 18.095 18624 Z= 0.560 Chirality : 0.053 0.395 2101 Planarity : 0.087 0.605 2046 Dihedral : 20.421 109.319 5956 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.67 % 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: -1.03 (0.25), residues: 1314 helix: -1.62 (0.57), residues: 88 sheet: -1.58 (0.39), residues: 224 loop : -0.34 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 452 HIS 0.007 0.001 HIS A 684 PHE 0.013 0.002 PHE B 71 TYR 0.011 0.002 TYR A 468 ARG 0.004 0.001 ARG A 643 *********************** 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 75 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.283 Fit side-chains REVERT: A 583 LYS cc_start: 0.8053 (pttt) cc_final: 0.7444 (tptt) REVERT: B 583 LYS cc_start: 0.8076 (pttt) cc_final: 0.7480 (tptt) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.2087 time to fit residues: 25.3247 Evaluate side-chains 64 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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: 0.7980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13410 Z= 0.289 Angle : 2.057 18.433 18624 Z= 1.246 Chirality : 0.046 0.434 2101 Planarity : 0.016 0.119 2046 Dihedral : 22.073 91.430 3356 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -1.09 (0.24), residues: 1314 helix: -1.21 (0.63), residues: 74 sheet: -1.73 (0.39), residues: 224 loop : -0.42 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.004 0.001 HIS B 60 PHE 0.014 0.001 PHE B 84 TYR 0.007 0.001 TYR A 468 ARG 0.003 0.000 ARG A 65 *********************** 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 70 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 LYS cc_start: 0.8087 (pttt) cc_final: 0.7457 (tptt) REVERT: B 583 LYS cc_start: 0.8088 (pttt) cc_final: 0.7477 (tptt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2055 time to fit residues: 23.5833 Evaluate side-chains 66 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13410 Z= 0.305 Angle : 1.889 16.387 18624 Z= 1.156 Chirality : 0.046 0.319 2101 Planarity : 0.017 0.122 2046 Dihedral : 22.414 101.576 3356 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % 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: -1.30 (0.24), residues: 1314 helix: -1.65 (0.59), residues: 74 sheet: -1.75 (0.41), residues: 200 loop : -0.62 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.004 0.001 HIS A 684 PHE 0.009 0.001 PHE A 606 TYR 0.008 0.001 TYR B 468 ARG 0.004 0.001 ARG B 65 *********************** 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 79 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.3493 (tpp) cc_final: 0.3228 (tpp) REVERT: B 100 MET cc_start: 0.3496 (tpp) cc_final: 0.3233 (tpp) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.2022 time to fit residues: 25.9645 Evaluate side-chains 67 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13410 Z= 0.369 Angle : 1.846 16.462 18624 Z= 1.145 Chirality : 0.047 0.320 2101 Planarity : 0.018 0.125 2046 Dihedral : 22.694 100.281 3356 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.41 % Allowed : 5.95 % Favored : 93.64 % 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: -1.62 (0.24), residues: 1314 helix: -2.09 (0.52), residues: 86 sheet: -1.89 (0.39), residues: 210 loop : -0.82 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.005 0.001 HIS A 684 PHE 0.011 0.001 PHE A 121 TYR 0.010 0.001 TYR B 468 ARG 0.003 0.001 ARG B 325 *********************** 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 70 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 70 average time/residue: 0.2077 time to fit residues: 23.7793 Evaluate side-chains 60 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13410 Z= 0.255 Angle : 1.781 15.496 18624 Z= 1.126 Chirality : 0.044 0.331 2101 Planarity : 0.017 0.122 2046 Dihedral : 22.714 101.612 3356 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.24 % Allowed : 7.42 % Favored : 92.33 % 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: -1.57 (0.24), residues: 1314 helix: -2.00 (0.53), residues: 86 sheet: -2.07 (0.38), residues: 224 loop : -0.70 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS B 548 PHE 0.008 0.001 PHE B 314 TYR 0.006 0.001 TYR A 468 ARG 0.002 0.000 ARG A 325 *********************** 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 76 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 0.1911 time to fit residues: 23.6640 Evaluate side-chains 67 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13410 Z= 0.345 Angle : 1.778 16.008 18624 Z= 1.121 Chirality : 0.047 0.311 2101 Planarity : 0.018 0.125 2046 Dihedral : 22.913 103.747 3356 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.73 % Allowed : 7.42 % Favored : 91.84 % 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: -1.68 (0.24), residues: 1314 helix: -1.62 (0.63), residues: 70 sheet: -1.96 (0.40), residues: 210 loop : -0.93 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 684 PHE 0.012 0.001 PHE B 121 TYR 0.008 0.001 TYR A 468 ARG 0.003 0.000 ARG A 453 *********************** 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 69 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5630 (mp) REVERT: B 49 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5636 (mp) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.2023 time to fit residues: 22.6172 Evaluate side-chains 66 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13410 Z= 0.196 Angle : 1.732 14.954 18624 Z= 1.112 Chirality : 0.043 0.336 2101 Planarity : 0.017 0.121 2046 Dihedral : 22.789 103.456 3356 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.65 % Allowed : 7.50 % Favored : 91.84 % 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: -1.46 (0.24), residues: 1314 helix: -1.33 (0.68), residues: 60 sheet: -2.11 (0.38), residues: 224 loop : -0.69 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 656 HIS 0.002 0.000 HIS A 548 PHE 0.007 0.001 PHE A 121 TYR 0.005 0.001 TYR A 468 ARG 0.002 0.000 ARG A 484 *********************** 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 75 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.2099 time to fit residues: 24.8771 Evaluate side-chains 66 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 38 SER 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: 0.8980 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13410 Z= 0.327 Angle : 1.744 15.486 18624 Z= 1.111 Chirality : 0.046 0.327 2101 Planarity : 0.018 0.124 2046 Dihedral : 22.962 103.907 3356 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.41 % Allowed : 8.89 % Favored : 90.70 % 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: -1.62 (0.24), residues: 1314 helix: -1.38 (0.68), residues: 60 sheet: -1.98 (0.40), residues: 210 loop : -0.89 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS A 684 PHE 0.010 0.001 PHE A 121 TYR 0.007 0.001 TYR A 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 66 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.2195 time to fit residues: 23.5501 Evaluate side-chains 60 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 679 THR 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: 0.8980 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13410 Z= 0.230 Angle : 1.718 14.858 18624 Z= 1.106 Chirality : 0.044 0.334 2101 Planarity : 0.017 0.122 2046 Dihedral : 22.903 103.437 3356 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.33 % Allowed : 9.22 % 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: -1.53 (0.24), residues: 1314 helix: -1.30 (0.69), residues: 60 sheet: -2.16 (0.38), residues: 224 loop : -0.74 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 684 PHE 0.010 0.001 PHE A 121 TYR 0.005 0.001 TYR A 468 ARG 0.001 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 70 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.2093 time to fit residues: 23.3797 Evaluate side-chains 64 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 679 THR 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: 4.9990 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 13410 Z= 0.399 Angle : 1.754 15.588 18624 Z= 1.113 Chirality : 0.048 0.305 2101 Planarity : 0.018 0.126 2046 Dihedral : 23.058 104.083 3356 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.33 % Allowed : 9.62 % Favored : 90.05 % 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: -1.80 (0.23), residues: 1314 helix: -1.30 (0.71), residues: 58 sheet: -2.08 (0.39), residues: 210 loop : -1.05 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.005 0.001 HIS A 684 PHE 0.012 0.001 PHE A 121 TYR 0.008 0.001 TYR A 468 ARG 0.003 0.001 ARG B 473 ********************** 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 68 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.2090 time to fit residues: 23.4402 Evaluate side-chains 57 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 679 THR 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: 0.9980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116709 restraints weight = 19159.927| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.26 r_work: 0.3502 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13410 Z= 0.211 Angle : 1.717 14.581 18624 Z= 1.106 Chirality : 0.043 0.325 2101 Planarity : 0.017 0.121 2046 Dihedral : 22.878 103.773 3356 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.33 % Allowed : 9.54 % Favored : 90.13 % 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: -1.61 (0.24), residues: 1314 helix: -1.29 (0.69), residues: 60 sheet: -2.08 (0.40), residues: 204 loop : -0.88 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 39 PHE 0.009 0.001 PHE B 121 TYR 0.005 0.001 TYR A 683 ARG 0.002 0.000 ARG B 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.88 seconds wall clock time: 50 minutes 49.33 seconds (3049.33 seconds total)