Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:15:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_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_32846/02_2023/7wv5_32846_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wv5_32846/02_2023/7wv5_32846_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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 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 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 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: 2 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 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 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 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 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: 2 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 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 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 chiralities: 5 Time building chain proxies: 10.59, per 1000 atoms: 0.82 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: 6.87 Conformation dependent library (CDL) restraints added in 1.7 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: 4.59 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: 4.12 Time building geometry restraints manager: 7.23 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 - 17.98: 7150 17.98 - 35.95: 368 35.95 - 53.93: 101 53.93 - 71.90: 125 71.90 - 89.88: 92 Dihedral angle restraints: 7836 sinusoidal: 3960 harmonic: 3876 Sorted by residual: dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual -180.00 -164.80 -15.20 0 5.00e+00 4.00e-02 9.24e+00 dihedral pdb=" CA ILE B 138 " pdb=" C ILE B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual -180.00 -164.87 -15.13 0 5.00e+00 4.00e-02 9.15e+00 dihedral pdb=" CA GLU B 306 " pdb=" CB GLU B 306 " pdb=" CG GLU B 306 " pdb=" CD GLU B 306 " ideal model delta sinusoidal sigma weight residual -60.00 -106.71 46.71 3 1.50e+01 4.44e-03 8.38e+00 ... (remaining 7833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1918 0.079 - 0.158: 174 0.158 - 0.237: 3 0.237 - 0.316: 0 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 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. 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: 8.920 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: 23.920 Check model and map are aligned: 0.200 Process input model: 43.400 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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= 1.011 Angle : 1.514 18.095 18624 Z= 0.553 Chirality : 0.050 0.395 2101 Planarity : 0.087 0.605 2046 Dihedral : 18.031 89.876 5288 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 % 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 *********************** 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 : 1.285 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.2114 time to fit residues: 25.5911 Evaluate side-chains 62 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8342 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.8063 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 13410 Z= 0.309 Angle : 2.073 18.986 18624 Z= 1.254 Chirality : 0.045 0.441 2101 Planarity : 0.016 0.119 2046 Dihedral : 20.343 89.552 2688 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.08 % 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: -1.15 (0.24), residues: 1314 helix: -1.73 (0.55), residues: 88 sheet: -1.73 (0.39), residues: 224 loop : -0.41 (0.21), residues: 1002 *********************** 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 71 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.2136 time to fit residues: 24.7126 Evaluate side-chains 65 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7612 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 13410 Z= 0.396 Angle : 1.907 16.767 18624 Z= 1.164 Chirality : 0.048 0.474 2101 Planarity : 0.017 0.124 2046 Dihedral : 21.675 101.335 2688 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.00 % 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: -1.45 (0.24), residues: 1314 helix: -1.72 (0.60), residues: 72 sheet: -1.88 (0.41), residues: 202 loop : -0.73 (0.20), residues: 1040 *********************** 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 75 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2090 time to fit residues: 26.0957 Evaluate side-chains 60 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9521 ------------------------------------------------------------------------------- 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: 0.6980 chunk 91 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 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: 0.7582 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13410 Z= 0.193 Angle : 1.812 15.909 18624 Z= 1.145 Chirality : 0.042 0.350 2101 Planarity : 0.017 0.119 2046 Dihedral : 21.996 98.745 2688 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.33 % 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: -1.32 (0.24), residues: 1314 helix: -1.82 (0.53), residues: 86 sheet: -1.93 (0.38), residues: 224 loop : -0.51 (0.21), residues: 1004 *********************** 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 77 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 77 average time/residue: 0.1973 time to fit residues: 25.7302 Evaluate side-chains 64 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9532 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.2380 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= 0.332 Angle : 1.802 16.198 18624 Z= 1.132 Chirality : 0.046 0.381 2101 Planarity : 0.017 0.124 2046 Dihedral : 22.341 100.451 2688 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.08 % 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: -1.89 (0.54), residues: 86 sheet: -1.84 (0.40), residues: 210 loop : -0.77 (0.20), residues: 1018 *********************** 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 65 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2164 time to fit residues: 22.8707 Evaluate side-chains 58 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7183 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.2400 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= 0.177 Angle : 1.757 15.305 18624 Z= 1.124 Chirality : 0.041 0.313 2101 Planarity : 0.017 0.120 2046 Dihedral : 22.296 101.302 2688 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.49 % 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: -1.35 (0.24), residues: 1314 helix: -1.75 (0.55), residues: 86 sheet: -1.94 (0.38), residues: 224 loop : -0.55 (0.21), residues: 1004 *********************** 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 74 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 72 average time/residue: 0.1978 time to fit residues: 23.9825 Evaluate side-chains 64 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8899 ------------------------------------------------------------------------------- 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: 0.6980 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13410 Z= 0.192 Angle : 1.721 14.918 18624 Z= 1.112 Chirality : 0.042 0.342 2101 Planarity : 0.017 0.119 2046 Dihedral : 22.601 102.084 2688 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.24 % 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: -1.27 (0.24), residues: 1314 helix: -1.58 (0.57), residues: 86 sheet: -1.89 (0.38), residues: 224 loop : -0.50 (0.21), residues: 1004 *********************** 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 71 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.1999 time to fit residues: 23.4158 Evaluate side-chains 66 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8008 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.040 13410 Z= 0.476 Angle : 1.772 16.287 18624 Z= 1.123 Chirality : 0.049 0.386 2101 Planarity : 0.018 0.129 2046 Dihedral : 22.677 103.305 2688 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer Outliers : 0.00 % 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: -1.76 (0.23), residues: 1314 helix: -1.35 (0.64), residues: 70 sheet: -1.95 (0.40), residues: 210 loop : -1.03 (0.19), residues: 1034 *********************** 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 63 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2020 time to fit residues: 21.7736 Evaluate side-chains 54 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8744 ------------------------------------------------------------------------------- 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: 0.9990 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 13410 Z= 0.206 Angle : 1.719 14.973 18624 Z= 1.110 Chirality : 0.042 0.302 2101 Planarity : 0.017 0.121 2046 Dihedral : 22.508 103.691 2688 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.08 % 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: -1.54 (0.24), residues: 1314 helix: -1.41 (0.62), residues: 72 sheet: -1.95 (0.40), residues: 204 loop : -0.82 (0.20), residues: 1038 *********************** 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 63 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2169 time to fit residues: 23.1130 Evaluate side-chains 61 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1193 time to fit residues: 2.0572 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 13410 Z= 0.317 Angle : 1.726 15.444 18624 Z= 1.110 Chirality : 0.045 0.322 2101 Planarity : 0.018 0.124 2046 Dihedral : 22.570 103.846 2688 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % 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: -1.60 (0.24), residues: 1314 helix: -1.11 (0.70), residues: 60 sheet: -1.87 (0.40), residues: 208 loop : -0.93 (0.20), residues: 1046 ********************** 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 56 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1944 time to fit residues: 18.9029 Evaluate side-chains 56 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7525 ------------------------------------------------------------------------------- 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: 0.8980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118480 restraints weight = 19168.383| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.31 r_work: 0.3535 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13410 Z= 0.188 Angle : 1.698 14.307 18624 Z= 1.104 Chirality : 0.041 0.307 2101 Planarity : 0.017 0.120 2046 Dihedral : 22.529 103.336 2688 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % 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: -1.44 (0.24), residues: 1314 helix: -1.29 (0.62), residues: 72 sheet: -1.91 (0.40), residues: 204 loop : -0.75 (0.20), residues: 1038 =============================================================================== Job complete usr+sys time: 2622.81 seconds wall clock time: 48 minutes 46.73 seconds (2926.73 seconds total)