Starting phenix.real_space_refine on Thu Feb 15 14:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wve_32851/02_2024/7wve_32851_updated.pdb" } resolution = 3.11 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= 0.029 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 7644 2.51 5 N 2120 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12498 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5286 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: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5286 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 917 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p_pyr': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1009 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna3p': 46} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Time building chain proxies: 7.28, per 1000 atoms: 0.58 Number of scatterers: 12498 At special positions: 0 Unit cell: (169.624, 92.1515, 94.598, 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 2610 8.00 N 2120 7.00 C 7644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 677 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 9.4% alpha, 8.2% beta 0 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 116 through 119 removed outlier: 3.929A pdb=" N PHE A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.675A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.703A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 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 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 96 Processing helix chain 'B' and resid 116 through 119 removed outlier: 3.930A pdb=" N PHE B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.675A pdb=" N ILE B 193 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.703A pdb=" N TRP B 273 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 543 through 546 No H-bonds generated for 'chain 'B' and resid 543 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 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: 6.580A 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: 6.725A pdb=" N VAL A 103 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 127 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 151 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 175 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.092A 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: 6.370A pdb=" N ASN A 252 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 302 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.204A 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 359 through 361 removed outlier: 6.219A pdb=" N TYR A 383 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE A 411 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 435 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU A 460 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG A 484 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 510 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 534 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 566 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 590 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER A 614 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.611A 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: 6.304A 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: 6.581A 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: 6.724A pdb=" N VAL B 103 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU B 127 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 151 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 175 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.092A 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: 6.371A pdb=" N ASN B 252 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET B 278 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR B 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.204A 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 359 through 361 removed outlier: 6.219A pdb=" N TYR B 383 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE B 411 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 435 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 460 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 534 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 566 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 590 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER B 614 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 6.610A 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: 6.305A pdb=" N TYR B 468 " --> pdb=" O GLN B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 36 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 6.06 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: 3720 1.34 - 1.46: 2939 1.46 - 1.58: 6061 1.58 - 1.69: 180 1.69 - 1.81: 50 Bond restraints: 12950 Sorted by residual: bond pdb=" C2 I F 20 " pdb=" N3 I F 20 " ideal model delta sigma weight residual 1.462 1.314 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C2 I F 21 " pdb=" N3 I F 21 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2 I F 31 " pdb=" N3 I F 31 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2 I F 28 " pdb=" N3 I F 28 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 I F 29 " pdb=" N3 I F 29 " ideal model delta sigma weight residual 1.462 1.315 0.147 2.00e-02 2.50e+03 5.41e+01 ... (remaining 12945 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.42: 811 107.42 - 114.05: 7825 114.05 - 120.69: 4681 120.69 - 127.33: 4365 127.33 - 133.97: 310 Bond angle restraints: 17992 Sorted by residual: angle pdb=" C1' I F 43 " pdb=" N9 I F 43 " pdb=" C4 I F 43 " ideal model delta sigma weight residual 106.08 123.91 -17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" C1' I F 5 " pdb=" N9 I F 5 " pdb=" C4 I F 5 " ideal model delta sigma weight residual 106.08 123.89 -17.81 3.00e+00 1.11e-01 3.52e+01 angle pdb=" C1' I F 37 " pdb=" N9 I F 37 " pdb=" C4 I F 37 " ideal model delta sigma weight residual 106.08 123.83 -17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" C1' I F 46 " pdb=" N9 I F 46 " pdb=" C4 I F 46 " ideal model delta sigma weight residual 106.08 123.79 -17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C1' I F 22 " pdb=" N9 I F 22 " pdb=" C4 I F 22 " ideal model delta sigma weight residual 106.08 123.78 -17.70 3.00e+00 1.11e-01 3.48e+01 ... (remaining 17987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7062 17.99 - 35.98: 313 35.98 - 53.97: 172 53.97 - 71.96: 122 71.96 - 89.95: 139 Dihedral angle restraints: 7808 sinusoidal: 3932 harmonic: 3876 Sorted by residual: 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 -165.56 -14.44 0 5.00e+00 4.00e-02 8.35e+00 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 -165.60 -14.40 0 5.00e+00 4.00e-02 8.29e+00 dihedral pdb=" CA GLU B 663 " pdb=" CB GLU B 663 " pdb=" CG GLU B 663 " pdb=" CD GLU B 663 " ideal model delta sinusoidal sigma weight residual 60.00 105.07 -45.07 3 1.50e+01 4.44e-03 8.10e+00 ... (remaining 7805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1155 0.026 - 0.052: 505 0.052 - 0.079: 164 0.079 - 0.105: 80 0.105 - 0.131: 27 Chirality restraints: 1931 Sorted by residual: chirality pdb=" CA ILE B 367 " pdb=" N ILE B 367 " pdb=" C ILE B 367 " pdb=" CB ILE B 367 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 367 " pdb=" N ILE A 367 " pdb=" C ILE A 367 " pdb=" CB ILE A 367 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 138 " pdb=" N ILE A 138 " pdb=" C ILE A 138 " pdb=" CB ILE A 138 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1928 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I F 20 " -0.219 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C2' I F 20 " 0.187 2.00e-02 2.50e+03 pdb=" C3' I F 20 " 0.594 2.00e-02 2.50e+03 pdb=" C4' I F 20 " -0.440 2.00e-02 2.50e+03 pdb=" C5' I F 20 " -0.055 2.00e-02 2.50e+03 pdb=" N9 I F 20 " 0.915 2.00e-02 2.50e+03 pdb=" O2' I F 20 " -0.960 2.00e-02 2.50e+03 pdb=" O3' I F 20 " 0.623 2.00e-02 2.50e+03 pdb=" O4' I F 20 " -0.646 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 19 " -0.217 2.00e-02 2.50e+03 5.92e-01 7.87e+03 pdb=" C2' I F 19 " 0.200 2.00e-02 2.50e+03 pdb=" C3' I F 19 " 0.592 2.00e-02 2.50e+03 pdb=" C4' I F 19 " -0.444 2.00e-02 2.50e+03 pdb=" C5' I F 19 " -0.045 2.00e-02 2.50e+03 pdb=" N9 I F 19 " 0.911 2.00e-02 2.50e+03 pdb=" O2' I F 19 " -0.937 2.00e-02 2.50e+03 pdb=" O3' I F 19 " 0.604 2.00e-02 2.50e+03 pdb=" O4' I F 19 " -0.664 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I F 27 " 0.220 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C2' I F 27 " -0.195 2.00e-02 2.50e+03 pdb=" C3' I F 27 " -0.593 2.00e-02 2.50e+03 pdb=" C4' I F 27 " 0.439 2.00e-02 2.50e+03 pdb=" C5' I F 27 " 0.048 2.00e-02 2.50e+03 pdb=" N9 I F 27 " -0.904 2.00e-02 2.50e+03 pdb=" O2' I F 27 " 0.945 2.00e-02 2.50e+03 pdb=" O3' I F 27 " -0.608 2.00e-02 2.50e+03 pdb=" O4' I F 27 " 0.647 2.00e-02 2.50e+03 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3075 2.80 - 3.32: 11087 3.32 - 3.85: 22128 3.85 - 4.37: 26668 4.37 - 4.90: 42370 Nonbonded interactions: 105328 Sorted by model distance: nonbonded pdb=" OD1 ASP B 81 " pdb=" ND2 ASN B 105 " model vdw 2.270 2.520 nonbonded pdb=" OD1 ASP A 81 " pdb=" ND2 ASN A 105 " model vdw 2.271 2.520 nonbonded pdb=" NE2 HIS A 108 " pdb=" O3' C E 5 " model vdw 2.275 2.520 nonbonded pdb=" OE1 GLU A 460 " pdb=" OH TYR A 462 " model vdw 2.306 2.440 nonbonded pdb=" OE1 GLU B 460 " pdb=" OH TYR B 462 " model vdw 2.307 2.440 ... (remaining 105323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.300 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 39.670 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.148 12950 Z= 0.801 Angle : 1.479 17.827 17992 Z= 0.522 Chirality : 0.037 0.131 1931 Planarity : 0.087 0.596 2010 Dihedral : 19.667 89.951 5260 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % 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: -0.88 (0.25), residues: 1314 helix: 0.05 (0.70), residues: 72 sheet: -1.64 (0.40), residues: 216 loop : -0.37 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 546 HIS 0.002 0.000 HIS A 359 PHE 0.006 0.001 PHE A 390 TYR 0.005 0.001 TYR A 468 ARG 0.001 0.000 ARG B 484 *********************** 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 174 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6724 (mtpt) cc_final: 0.6304 (tptp) REVERT: A 100 MET cc_start: 0.5722 (mmp) cc_final: 0.4947 (ptt) REVERT: A 172 ASN cc_start: 0.6870 (m-40) cc_final: 0.6651 (t0) REVERT: A 314 PHE cc_start: 0.7745 (m-80) cc_final: 0.7297 (m-80) REVERT: B 42 LEU cc_start: 0.6846 (mp) cc_final: 0.6523 (mp) REVERT: B 100 MET cc_start: 0.5464 (mmp) cc_final: 0.4963 (mmp) REVERT: B 144 VAL cc_start: 0.7322 (p) cc_final: 0.6996 (p) REVERT: B 196 ASN cc_start: 0.7420 (t0) cc_final: 0.7091 (m-40) REVERT: B 398 ASN cc_start: 0.5909 (p0) cc_final: 0.5576 (t0) REVERT: B 418 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7960 (mttp) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.2445 time to fit residues: 61.0073 Evaluate side-chains 105 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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: 0.6980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 608 ASN A 682 HIS B 61 ASN B 107 GLN B 156 HIS B 230 ASN B 308 ASN B 608 ASN B 682 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12950 Z= 0.357 Angle : 1.933 16.554 17992 Z= 1.208 Chirality : 0.043 0.148 1931 Planarity : 0.017 0.128 2010 Dihedral : 24.434 96.919 2650 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.47 % Allowed : 9.05 % Favored : 89.48 % 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: -1.06 (0.24), residues: 1314 helix: 0.23 (0.70), residues: 72 sheet: -1.96 (0.38), residues: 216 loop : -0.47 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.005 0.001 HIS A 682 PHE 0.016 0.002 PHE A 375 TYR 0.009 0.001 TYR B 307 ARG 0.005 0.001 ARG A 331 *********************** 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 127 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.452 Fit side-chains REVERT: A 41 LYS cc_start: 0.6778 (mtpt) cc_final: 0.6370 (tptp) REVERT: A 100 MET cc_start: 0.5915 (mmp) cc_final: 0.5090 (ptt) REVERT: A 172 ASN cc_start: 0.7254 (m-40) cc_final: 0.6861 (t0) REVERT: B 37 CYS cc_start: 0.7284 (m) cc_final: 0.6415 (t) REVERT: B 42 LEU cc_start: 0.6887 (mp) cc_final: 0.6444 (mp) REVERT: B 100 MET cc_start: 0.5396 (mmp) cc_final: 0.4929 (mmp) REVERT: B 196 ASN cc_start: 0.7517 (t0) cc_final: 0.7172 (m-40) REVERT: B 314 PHE cc_start: 0.7795 (m-80) cc_final: 0.7293 (m-80) REVERT: B 418 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7977 (mttp) REVERT: B 510 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 663 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6694 (pp20) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 0.2351 time to fit residues: 42.6420 Evaluate side-chains 104 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS B 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12950 Z= 0.389 Angle : 1.841 14.767 17992 Z= 1.148 Chirality : 0.044 0.142 1931 Planarity : 0.018 0.129 2010 Dihedral : 24.672 91.600 2650 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.61 % Allowed : 10.85 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1314 helix: -0.96 (0.62), residues: 84 sheet: -2.21 (0.37), residues: 212 loop : -0.70 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.005 0.001 HIS A 312 PHE 0.015 0.002 PHE A 212 TYR 0.009 0.001 TYR B 468 ARG 0.004 0.001 ARG B 331 *********************** 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 124 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.345 Fit side-chains REVERT: A 41 LYS cc_start: 0.6719 (mtpt) cc_final: 0.6341 (tptp) REVERT: A 81 ASP cc_start: 0.7008 (t0) cc_final: 0.6803 (t0) REVERT: A 100 MET cc_start: 0.5839 (mmp) cc_final: 0.4933 (ptt) REVERT: A 172 ASN cc_start: 0.7583 (m-40) cc_final: 0.7373 (t0) REVERT: A 182 LYS cc_start: 0.7182 (mtmt) cc_final: 0.6782 (mmtt) REVERT: A 229 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7517 (m-40) REVERT: A 418 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7898 (mttp) REVERT: A 663 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: B 37 CYS cc_start: 0.7283 (m) cc_final: 0.6541 (t) REVERT: B 42 LEU cc_start: 0.6948 (mp) cc_final: 0.6510 (mp) REVERT: B 100 MET cc_start: 0.5411 (mmp) cc_final: 0.4941 (mmp) REVERT: B 172 ASN cc_start: 0.7497 (m-40) cc_final: 0.7033 (t0) REVERT: B 196 ASN cc_start: 0.7663 (t0) cc_final: 0.7251 (m-40) REVERT: B 229 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7904 (m-40) REVERT: B 314 PHE cc_start: 0.7916 (m-80) cc_final: 0.7700 (m-80) REVERT: B 418 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7912 (mttp) REVERT: B 510 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 663 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6667 (pp20) outliers start: 32 outliers final: 16 residues processed: 115 average time/residue: 0.2219 time to fit residues: 38.7957 Evaluate side-chains 101 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.0570 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12950 Z= 0.175 Angle : 1.766 15.114 17992 Z= 1.135 Chirality : 0.039 0.135 1931 Planarity : 0.017 0.121 2010 Dihedral : 24.829 93.366 2650 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 11.75 % Favored : 86.22 % 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: -0.70 (0.62), residues: 84 sheet: -2.15 (0.37), residues: 216 loop : -0.59 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 452 HIS 0.003 0.001 HIS B 359 PHE 0.018 0.001 PHE A 304 TYR 0.005 0.001 TYR A 468 ARG 0.004 0.000 ARG A 489 *********************** 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 113 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.482 Fit side-chains REVERT: A 41 LYS cc_start: 0.6815 (mtpt) cc_final: 0.6448 (tptp) REVERT: A 81 ASP cc_start: 0.6871 (t0) cc_final: 0.6624 (t0) REVERT: A 100 MET cc_start: 0.5807 (mmp) cc_final: 0.4839 (ptp) REVERT: A 418 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7810 (mttp) REVERT: A 663 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: B 37 CYS cc_start: 0.7357 (m) cc_final: 0.6587 (t) REVERT: B 42 LEU cc_start: 0.6840 (mp) cc_final: 0.6555 (mp) REVERT: B 100 MET cc_start: 0.5365 (mmp) cc_final: 0.4878 (mmp) REVERT: B 172 ASN cc_start: 0.7481 (m-40) cc_final: 0.7065 (t0) REVERT: B 196 ASN cc_start: 0.7589 (t0) cc_final: 0.7205 (m-40) REVERT: B 398 ASN cc_start: 0.5893 (p0) cc_final: 0.5446 (t0) REVERT: B 418 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7884 (mttp) REVERT: B 663 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6679 (pp20) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.2056 time to fit residues: 33.7518 Evaluate side-chains 96 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 312 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 12950 Z= 0.614 Angle : 1.847 15.206 17992 Z= 1.151 Chirality : 0.049 0.152 1931 Planarity : 0.018 0.138 2010 Dihedral : 24.986 90.345 2650 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.02 % Allowed : 12.81 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.22), residues: 1314 helix: -1.44 (0.59), residues: 84 sheet: -2.60 (0.36), residues: 210 loop : -1.13 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.007 0.002 HIS B 312 PHE 0.018 0.003 PHE A 401 TYR 0.012 0.002 TYR A 675 ARG 0.004 0.001 ARG B 489 *********************** 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 127 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 1.342 Fit side-chains REVERT: A 41 LYS cc_start: 0.6970 (mtpt) cc_final: 0.6571 (tptp) REVERT: A 100 MET cc_start: 0.5942 (mmp) cc_final: 0.5072 (pmm) REVERT: A 182 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7187 (mmtt) REVERT: A 418 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7925 (mttp) REVERT: A 663 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6755 (pp20) REVERT: B 37 CYS cc_start: 0.7394 (m) cc_final: 0.6623 (t) REVERT: B 42 LEU cc_start: 0.6962 (mp) cc_final: 0.6479 (mp) REVERT: B 100 MET cc_start: 0.5439 (mmp) cc_final: 0.4997 (pmm) REVERT: B 137 LYS cc_start: 0.8307 (tttm) cc_final: 0.8067 (tppt) REVERT: B 172 ASN cc_start: 0.7614 (m-40) cc_final: 0.7245 (t0) REVERT: B 177 LEU cc_start: 0.7938 (mp) cc_final: 0.7457 (mp) REVERT: B 196 ASN cc_start: 0.7746 (t0) cc_final: 0.7357 (m-40) REVERT: B 287 ASN cc_start: 0.7599 (t0) cc_final: 0.7118 (t0) REVERT: B 306 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: B 311 GLN cc_start: 0.7472 (mt0) cc_final: 0.7004 (mt0) REVERT: B 418 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8006 (mttp) REVERT: B 663 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6707 (pp20) outliers start: 37 outliers final: 25 residues processed: 117 average time/residue: 0.2137 time to fit residues: 38.9274 Evaluate side-chains 106 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12950 Z= 0.178 Angle : 1.756 14.988 17992 Z= 1.130 Chirality : 0.039 0.147 1931 Planarity : 0.017 0.122 2010 Dihedral : 24.996 90.564 2650 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 12.89 % Favored : 84.34 % 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: -0.86 (0.60), residues: 84 sheet: -2.46 (0.37), residues: 226 loop : -0.75 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 452 HIS 0.004 0.001 HIS B 359 PHE 0.016 0.001 PHE B 304 TYR 0.004 0.001 TYR A 468 ARG 0.003 0.000 ARG A 489 *********************** 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 118 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.5957 (mmp) cc_final: 0.5116 (pmm) REVERT: A 182 LYS cc_start: 0.7372 (mtmt) cc_final: 0.6991 (mmtt) REVERT: A 244 GLU cc_start: 0.7488 (tp30) cc_final: 0.7234 (tp30) REVERT: A 311 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: A 418 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7845 (mttp) REVERT: A 663 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: B 42 LEU cc_start: 0.6838 (mp) cc_final: 0.6370 (tp) REVERT: B 100 MET cc_start: 0.5395 (mmp) cc_final: 0.5105 (mmp) REVERT: B 137 LYS cc_start: 0.8249 (tttm) cc_final: 0.7978 (tppt) REVERT: B 172 ASN cc_start: 0.7587 (m-40) cc_final: 0.7109 (t0) REVERT: B 196 ASN cc_start: 0.7645 (t0) cc_final: 0.7228 (m-40) REVERT: B 418 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7964 (mttp) REVERT: B 663 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6662 (pp20) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.2065 time to fit residues: 34.3511 Evaluate side-chains 107 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 78 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12950 Z= 0.336 Angle : 1.762 14.828 17992 Z= 1.128 Chirality : 0.042 0.140 1931 Planarity : 0.018 0.128 2010 Dihedral : 25.095 89.819 2650 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.26 % Allowed : 13.30 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.23), residues: 1314 helix: -0.96 (0.60), residues: 84 sheet: -2.56 (0.37), residues: 216 loop : -0.87 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.003 0.001 HIS A 312 PHE 0.011 0.002 PHE A 375 TYR 0.006 0.001 TYR B 468 ARG 0.004 0.000 ARG A 489 *********************** 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 125 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.5917 (mmp) cc_final: 0.4994 (pmm) REVERT: A 182 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7193 (mmtt) REVERT: A 229 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: A 418 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7904 (mttp) REVERT: A 663 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6701 (pp20) REVERT: B 42 LEU cc_start: 0.6839 (mp) cc_final: 0.6360 (tp) REVERT: B 100 MET cc_start: 0.5489 (mmp) cc_final: 0.5200 (mmp) REVERT: B 137 LYS cc_start: 0.8296 (tttm) cc_final: 0.8040 (tppt) REVERT: B 172 ASN cc_start: 0.7557 (m-40) cc_final: 0.7120 (t0) REVERT: B 177 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7291 (mp) REVERT: B 196 ASN cc_start: 0.7674 (t0) cc_final: 0.7268 (m-40) REVERT: B 229 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: B 418 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8014 (mttp) REVERT: B 425 ASP cc_start: 0.7402 (m-30) cc_final: 0.7169 (m-30) REVERT: B 663 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6704 (pp20) outliers start: 40 outliers final: 24 residues processed: 113 average time/residue: 0.2029 time to fit residues: 36.0853 Evaluate side-chains 108 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 79 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12950 Z= 0.313 Angle : 1.752 14.396 17992 Z= 1.125 Chirality : 0.042 0.137 1931 Planarity : 0.018 0.127 2010 Dihedral : 25.074 89.961 2650 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.69 % Allowed : 14.19 % Favored : 83.12 % 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: -1.78 (0.23), residues: 1314 helix: -0.89 (0.60), residues: 84 sheet: -2.57 (0.37), residues: 226 loop : -0.89 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.003 0.001 HIS A 359 PHE 0.012 0.002 PHE A 401 TYR 0.006 0.001 TYR B 468 ARG 0.004 0.000 ARG A 489 *********************** 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 114 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.5945 (mmp) cc_final: 0.4972 (pmm) REVERT: A 182 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7182 (mmtt) REVERT: A 229 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7701 (m-40) REVERT: A 418 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7873 (mttp) REVERT: A 663 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6696 (pp20) REVERT: B 42 LEU cc_start: 0.6835 (mp) cc_final: 0.6354 (tp) REVERT: B 90 LEU cc_start: 0.8304 (mp) cc_final: 0.8090 (mp) REVERT: B 100 MET cc_start: 0.5852 (mmp) cc_final: 0.5013 (pmm) REVERT: B 137 LYS cc_start: 0.8295 (tttm) cc_final: 0.8015 (tppt) REVERT: B 172 ASN cc_start: 0.7600 (m-40) cc_final: 0.7187 (t0) REVERT: B 196 ASN cc_start: 0.7666 (t0) cc_final: 0.7263 (m-40) REVERT: B 229 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: B 418 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7994 (mttp) REVERT: B 425 ASP cc_start: 0.7319 (m-30) cc_final: 0.7080 (m-30) REVERT: B 663 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6709 (pp20) outliers start: 33 outliers final: 26 residues processed: 105 average time/residue: 0.2023 time to fit residues: 34.0278 Evaluate side-chains 108 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12950 Z= 0.227 Angle : 1.728 13.817 17992 Z= 1.120 Chirality : 0.040 0.135 1931 Planarity : 0.017 0.123 2010 Dihedral : 25.045 89.952 2650 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.02 % Allowed : 13.95 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.24), residues: 1314 helix: -0.70 (0.61), residues: 84 sheet: -2.59 (0.36), residues: 228 loop : -0.84 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 452 HIS 0.003 0.001 HIS A 359 PHE 0.011 0.001 PHE B 304 TYR 0.005 0.001 TYR B 468 ARG 0.004 0.000 ARG A 489 *********************** 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 120 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 83 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.5942 (mmp) cc_final: 0.4905 (pmm) REVERT: A 182 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7198 (mmtt) REVERT: A 229 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7510 (m-40) REVERT: A 418 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7870 (mttp) REVERT: A 663 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6716 (pp20) REVERT: B 42 LEU cc_start: 0.6825 (mp) cc_final: 0.6412 (tp) REVERT: B 90 LEU cc_start: 0.8308 (mp) cc_final: 0.8101 (mp) REVERT: B 100 MET cc_start: 0.5770 (mmp) cc_final: 0.5007 (pmm) REVERT: B 137 LYS cc_start: 0.8309 (tttm) cc_final: 0.8042 (tppt) REVERT: B 172 ASN cc_start: 0.7567 (m-40) cc_final: 0.7185 (t0) REVERT: B 196 ASN cc_start: 0.7613 (t0) cc_final: 0.7222 (m-40) REVERT: B 229 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7760 (m-40) REVERT: B 418 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7978 (mttp) REVERT: B 425 ASP cc_start: 0.7283 (m-30) cc_final: 0.7071 (m-30) REVERT: B 663 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6722 (pp20) outliers start: 37 outliers final: 26 residues processed: 112 average time/residue: 0.1967 time to fit residues: 35.4774 Evaluate side-chains 111 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain B residue 666 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 122 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 30.0000 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12950 Z= 0.302 Angle : 1.740 13.985 17992 Z= 1.122 Chirality : 0.041 0.135 1931 Planarity : 0.018 0.127 2010 Dihedral : 25.080 89.895 2650 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.69 % Allowed : 14.36 % Favored : 82.95 % 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: -1.87 (0.23), residues: 1314 helix: -0.88 (0.56), residues: 96 sheet: -2.61 (0.37), residues: 228 loop : -0.96 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.007 0.001 HIS B 39 PHE 0.011 0.001 PHE A 401 TYR 0.005 0.001 TYR B 468 ARG 0.004 0.000 ARG A 489 ********************** 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 116 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 1.320 Fit side-chains REVERT: A 100 MET cc_start: 0.5972 (mmp) cc_final: 0.4962 (pmm) REVERT: A 182 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7261 (mmtt) REVERT: A 229 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7702 (m-40) REVERT: A 418 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7880 (mttp) REVERT: A 663 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6703 (pp20) REVERT: B 39 HIS cc_start: 0.7870 (m90) cc_final: 0.7643 (m90) REVERT: B 42 LEU cc_start: 0.6885 (mp) cc_final: 0.6421 (tp) REVERT: B 90 LEU cc_start: 0.8394 (mp) cc_final: 0.8171 (mp) REVERT: B 100 MET cc_start: 0.5746 (mmp) cc_final: 0.4812 (pmm) REVERT: B 137 LYS cc_start: 0.8300 (tttm) cc_final: 0.7864 (mmtm) REVERT: B 172 ASN cc_start: 0.7573 (m-40) cc_final: 0.7221 (t0) REVERT: B 196 ASN cc_start: 0.7646 (t0) cc_final: 0.7247 (m-40) REVERT: B 229 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7786 (m-40) REVERT: B 418 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7988 (mttp) REVERT: B 425 ASP cc_start: 0.7342 (m-30) cc_final: 0.7108 (m-30) REVERT: B 663 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6731 (pp20) outliers start: 33 outliers final: 25 residues processed: 108 average time/residue: 0.2077 time to fit residues: 35.9217 Evaluate side-chains 109 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain B residue 666 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115903 restraints weight = 16270.125| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.10 r_work: 0.3376 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12950 Z= 0.283 Angle : 1.734 13.991 17992 Z= 1.120 Chirality : 0.041 0.136 1931 Planarity : 0.018 0.126 2010 Dihedral : 25.068 89.599 2650 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 14.36 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1314 helix: -0.88 (0.56), residues: 96 sheet: -2.60 (0.37), residues: 228 loop : -0.96 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.003 0.001 HIS A 359 PHE 0.010 0.001 PHE A 401 TYR 0.005 0.001 TYR B 468 ARG 0.004 0.000 ARG A 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.11 seconds wall clock time: 51 minutes 20.41 seconds (3080.41 seconds total)