Starting phenix.real_space_refine on Mon Jun 24 23:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enq_19838/06_2024/9enq_19838_neut_updated.pdb" } resolution = 2.12 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= 0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 6 5.49 5 S 32 5.16 5 C 3652 2.51 5 N 995 2.21 5 O 1056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 5743 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 707, 5587 Classifications: {'peptide': 707} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 671} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 707, 5587 Classifications: {'peptide': 707} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 671} Chain breaks: 2 bond proxies already assigned to first conformer: 5696 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' AS': 2} Classifications: {'DNA': 2, 'undetermined': 2} Link IDs: {'rna3p': 1, None: 2} Not linked: pdbres=" DC C 21 " pdbres=" AS C 22 " Not linked: pdbres=" AS C 22 " pdbres=" AS C 23 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "A" Number of atoms: 9 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Conformer: "B" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'water': 6} Link IDs: {None: 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 577 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 577 " occ=0.50 residue: pdb=" N AGLN A 580 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 580 " occ=0.50 residue: pdb=" O AHOH A1405 " occ=0.50 pdb=" O BHOH A1405 " occ=0.50 Time building chain proxies: 8.55, per 1000 atoms: 1.49 Number of scatterers: 5743 At special positions: 0 Unit cell: (80, 112.8, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 32 16.00 P 6 15.00 O 1056 8.00 N 995 7.00 C 3652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 7 sheets defined 36.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.686A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.555A pdb=" N CYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 557 through 566 Proline residue: A 561 - end of helix Processing helix chain 'A' and resid 568 through 592 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 618 through 632 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 773 through 794 Proline residue: A 793 - end of helix Processing helix chain 'A' and resid 797 through 822 removed outlier: 3.750A pdb=" N VAL A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 Processing sheet with id= A, first strand: chain 'A' and resid 74 through 79 Processing sheet with id= B, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 350 through 352 removed outlier: 7.047A pdb=" N LEU A 185 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 152 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR A 183 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU A 154 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 181 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 156 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY A 179 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 341 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS A 197 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 343 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR A 199 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS A 345 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.607A pdb=" N GLN A 203 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 521 through 524 removed outlier: 4.034A pdb=" N GLY A 464 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 436 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 413 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 438 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 499 through 502 Processing sheet with id= G, first strand: chain 'A' and resid 752 through 757 223 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 1924 1.37 - 1.52: 1860 1.52 - 1.67: 2052 1.67 - 1.82: 42 1.82 - 1.97: 4 Bond restraints: 5882 Sorted by residual: bond pdb=" C2' AS C 23 " pdb=" C3' AS C 23 " ideal model delta sigma weight residual 1.222 1.529 -0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C2' AS C 22 " pdb=" C3' AS C 22 " ideal model delta sigma weight residual 1.222 1.517 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C4' AS C 23 " pdb=" O4' AS C 23 " ideal model delta sigma weight residual 1.267 1.443 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C4' AS C 22 " pdb=" O4' AS C 22 " ideal model delta sigma weight residual 1.267 1.442 -0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" OP1 AS C 22 " pdb=" P AS C 22 " ideal model delta sigma weight residual 1.649 1.492 0.157 2.00e-02 2.50e+03 6.14e+01 ... (remaining 5877 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.66: 184 105.66 - 113.00: 2815 113.00 - 120.35: 2640 120.35 - 127.69: 2305 127.69 - 135.03: 51 Bond angle restraints: 7995 Sorted by residual: angle pdb=" CA ASP A 298 " pdb=" CB ASP A 298 " pdb=" CG ASP A 298 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" NE ARG A 91 " pdb=" CZ ARG A 91 " pdb=" NH2 ARG A 91 " ideal model delta sigma weight residual 119.20 114.14 5.06 9.00e-01 1.23e+00 3.16e+01 angle pdb=" CA ASP A 257 " pdb=" CB ASP A 257 " pdb=" CG ASP A 257 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" N1 AS C 23 " pdb=" C6 AS C 23 " pdb=" N6 AS C 23 " ideal model delta sigma weight residual 104.68 119.34 -14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" C ASP A 559 " pdb=" N ILE A 560 " pdb=" CA ILE A 560 " ideal model delta sigma weight residual 120.33 124.21 -3.88 8.00e-01 1.56e+00 2.35e+01 ... (remaining 7990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3238 17.43 - 34.86: 162 34.86 - 52.28: 44 52.28 - 69.71: 22 69.71 - 87.14: 6 Dihedral angle restraints: 3472 sinusoidal: 1419 harmonic: 2053 Sorted by residual: dihedral pdb=" CD ARG A 91 " pdb=" NE ARG A 91 " pdb=" CZ ARG A 91 " pdb=" NH1 ARG A 91 " ideal model delta sinusoidal sigma weight residual 0.00 50.92 -50.92 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CA LEU A 390 " pdb=" C LEU A 390 " pdb=" N VAL A 391 " pdb=" CA VAL A 391 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU A 753 " pdb=" C LEU A 753 " pdb=" N GLU A 754 " pdb=" CA GLU A 754 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 754 0.126 - 0.252: 113 0.252 - 0.378: 3 0.378 - 0.504: 0 0.504 - 0.630: 2 Chirality restraints: 872 Sorted by residual: chirality pdb=" P DG D -15 " pdb=" OP1 DG D -15 " pdb=" OP2 DG D -15 " pdb=" O5' DG D -15 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" P DT C 20 " pdb=" OP1 DT C 20 " pdb=" OP2 DT C 20 " pdb=" O5' DT C 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" CA TYR A 260 " pdb=" N TYR A 260 " pdb=" C TYR A 260 " pdb=" CB TYR A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 869 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AS C 23 " 0.332 2.00e-02 2.50e+03 5.22e-01 5.46e+03 pdb=" C2' AS C 23 " -0.653 2.00e-02 2.50e+03 pdb=" C3' AS C 23 " -0.438 2.00e-02 2.50e+03 pdb=" C4' AS C 23 " 0.306 2.00e-02 2.50e+03 pdb=" C5' AS C 23 " -0.553 2.00e-02 2.50e+03 pdb=" N9 AS C 23 " -0.276 2.00e-02 2.50e+03 pdb=" O3' AS C 23 " 0.359 2.00e-02 2.50e+03 pdb=" O4' AS C 23 " 0.923 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AS C 22 " 0.414 2.00e-02 2.50e+03 3.49e-01 2.44e+03 pdb=" C2' AS C 22 " 0.281 2.00e-02 2.50e+03 pdb=" C3' AS C 22 " -0.347 2.00e-02 2.50e+03 pdb=" C4' AS C 22 " 0.336 2.00e-02 2.50e+03 pdb=" C5' AS C 22 " -0.286 2.00e-02 2.50e+03 pdb=" N9 AS C 22 " -0.590 2.00e-02 2.50e+03 pdb=" O3' AS C 22 " -0.052 2.00e-02 2.50e+03 pdb=" O4' AS C 22 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " 0.964 9.50e-02 1.11e+02 4.33e-01 1.26e+02 pdb=" NE ARG A 91 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " 0.045 2.00e-02 2.50e+03 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1373 2.82 - 3.34: 5156 3.34 - 3.86: 10013 3.86 - 4.38: 11723 4.38 - 4.90: 19574 Nonbonded interactions: 47839 Sorted by model distance: nonbonded pdb=" O VAL A 81 " pdb=" NH2 ARG A 91 " model vdw 2.294 2.520 nonbonded pdb="CA CA A1302 " pdb=" O HOH A1402 " model vdw 2.300 2.510 nonbonded pdb=" OD1 ASP A 368 " pdb="CA CA A1301 " model vdw 2.338 2.510 nonbonded pdb=" OD1 ASN A 466 " pdb=" O HOH A1401 " model vdw 2.370 2.440 nonbonded pdb=" OP1 AS C 23 " pdb=" O HOH C 101 " model vdw 2.403 2.440 ... (remaining 47834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 6.470 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: 22.070 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.340 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.012 0.307 5882 Z= 0.883 Angle : 1.397 14.662 7995 Z= 0.890 Chirality : 0.087 0.630 872 Planarity : 0.026 0.522 1019 Dihedral : 13.434 87.140 2160 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.45 (0.29), residues: 707 helix: -0.44 (0.30), residues: 275 sheet: 0.07 (0.40), residues: 126 loop : -0.09 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.009 TRP A 472 HIS 0.031 0.004 HIS A 729 PHE 0.033 0.007 PHE A 590 TYR 0.040 0.008 TYR A 490 ARG 0.062 0.003 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.599 Fit side-chains REVERT: A 70 GLU cc_start: 0.7736 (pm20) cc_final: 0.7256 (pp20) REVERT: A 72 ASP cc_start: 0.7361 (p0) cc_final: 0.6699 (m-30) REVERT: A 73 GLU cc_start: 0.7180 (pp20) cc_final: 0.6914 (pm20) REVERT: A 100 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6943 (mmtm) REVERT: A 110 ASP cc_start: 0.7782 (m-30) cc_final: 0.7512 (m-30) REVERT: A 264 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6187 (mmm160) REVERT: A 353 GLU cc_start: 0.7337 (tp30) cc_final: 0.7074 (tp30) REVERT: A 356 MET cc_start: 0.7373 (mtp) cc_final: 0.7084 (mtm) REVERT: A 421 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6915 (mm-30) REVERT: A 426 GLU cc_start: 0.7776 (tt0) cc_final: 0.7483 (tt0) REVERT: A 541 ASN cc_start: 0.7648 (t0) cc_final: 0.6965 (p0) REVERT: A 597 GLU cc_start: 0.8103 (pt0) cc_final: 0.6991 (tp30) REVERT: A 617 GLN cc_start: 0.7956 (mt0) cc_final: 0.6618 (pp30) REVERT: A 630 ASP cc_start: 0.7238 (t70) cc_final: 0.6636 (m-30) REVERT: A 741 ASP cc_start: 0.7028 (p0) cc_final: 0.6764 (p0) REVERT: A 756 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6979 (tp30) REVERT: A 760 ARG cc_start: 0.6424 (mtp180) cc_final: 0.5830 (ttm-80) REVERT: A 761 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.7313 (ttp-110) REVERT: A 787 GLN cc_start: 0.7356 (tt0) cc_final: 0.6946 (tm-30) REVERT: A 824 GLN cc_start: 0.6665 (tt0) cc_final: 0.6045 (tp40) REVERT: A 842 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7339 (mtm-85) REVERT: A 843 GLU cc_start: 0.7268 (tp30) cc_final: 0.6620 (mp0) REVERT: A 844 MET cc_start: 0.8095 (mtp) cc_final: 0.7792 (mtm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 1.3140 time to fit residues: 130.1267 Evaluate side-chains 75 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 ASN A 825 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5882 Z= 0.244 Angle : 0.885 19.868 7995 Z= 0.400 Chirality : 0.047 0.172 872 Planarity : 0.005 0.045 1019 Dihedral : 11.516 83.579 846 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.84 % Allowed : 5.38 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.54 (0.30), residues: 707 helix: 0.92 (0.32), residues: 275 sheet: 0.10 (0.40), residues: 116 loop : 0.12 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 130 HIS 0.012 0.002 HIS A 98 PHE 0.020 0.002 PHE A 444 TYR 0.021 0.002 TYR A 490 ARG 0.004 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.627 Fit side-chains REVERT: A 70 GLU cc_start: 0.7706 (pm20) cc_final: 0.7164 (pp20) REVERT: A 72 ASP cc_start: 0.7533 (p0) cc_final: 0.6892 (m-30) REVERT: A 73 GLU cc_start: 0.7358 (pp20) cc_final: 0.6999 (pm20) REVERT: A 91 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6931 (mtp-110) REVERT: A 100 LYS cc_start: 0.7470 (mmtm) cc_final: 0.7019 (mmtm) REVERT: A 110 ASP cc_start: 0.7711 (m-30) cc_final: 0.7475 (m-30) REVERT: A 228 MET cc_start: 0.5214 (mtm) cc_final: 0.5004 (mtm) REVERT: A 353 GLU cc_start: 0.7467 (tp30) cc_final: 0.7195 (tp30) REVERT: A 421 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6902 (mm-30) REVERT: A 426 GLU cc_start: 0.7812 (tt0) cc_final: 0.7513 (tt0) REVERT: A 469 ASN cc_start: 0.7899 (m-40) cc_final: 0.7451 (m-40) REVERT: A 534 LYS cc_start: 0.6957 (mmtp) cc_final: 0.6402 (tptp) REVERT: A 541 ASN cc_start: 0.7654 (t0) cc_final: 0.6960 (p0) REVERT: A 597 GLU cc_start: 0.7892 (pt0) cc_final: 0.6750 (tp30) REVERT: A 617 GLN cc_start: 0.7980 (mt0) cc_final: 0.6631 (pp30) REVERT: A 618 GLN cc_start: 0.8158 (mt0) cc_final: 0.7414 (mm110) REVERT: A 630 ASP cc_start: 0.7346 (t70) cc_final: 0.6544 (m-30) REVERT: A 741 ASP cc_start: 0.7069 (p0) cc_final: 0.6822 (p0) REVERT: A 754 GLU cc_start: 0.7879 (pt0) cc_final: 0.7604 (tt0) REVERT: A 756 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6949 (mm-30) REVERT: A 760 ARG cc_start: 0.6415 (mtp180) cc_final: 0.5807 (ttt-90) REVERT: A 761 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7360 (ttp-110) REVERT: A 787 GLN cc_start: 0.7195 (tt0) cc_final: 0.6820 (tm-30) REVERT: A 811 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7856 (tttp) REVERT: A 824 GLN cc_start: 0.6763 (tt0) cc_final: 0.6117 (tp40) REVERT: A 842 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7334 (mtm-85) REVERT: A 843 GLU cc_start: 0.7240 (tp30) cc_final: 0.6534 (mp0) REVERT: A 844 MET cc_start: 0.8028 (mtp) cc_final: 0.7751 (mtm) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 1.4611 time to fit residues: 126.2040 Evaluate side-chains 79 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 56 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN A 815 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5882 Z= 0.227 Angle : 0.832 16.044 7995 Z= 0.377 Chirality : 0.045 0.163 872 Planarity : 0.005 0.031 1019 Dihedral : 11.240 78.179 846 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.01 % Allowed : 6.05 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.70 (0.30), residues: 707 helix: 1.17 (0.32), residues: 276 sheet: -0.04 (0.41), residues: 116 loop : 0.18 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 130 HIS 0.010 0.002 HIS A 98 PHE 0.018 0.002 PHE A 590 TYR 0.021 0.002 TYR A 490 ARG 0.007 0.001 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.633 Fit side-chains REVERT: A 70 GLU cc_start: 0.7697 (pm20) cc_final: 0.7127 (pp20) REVERT: A 72 ASP cc_start: 0.7420 (p0) cc_final: 0.6877 (m-30) REVERT: A 73 GLU cc_start: 0.7363 (pp20) cc_final: 0.6968 (pm20) REVERT: A 91 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6869 (mtp-110) REVERT: A 100 LYS cc_start: 0.7480 (mmtm) cc_final: 0.7017 (mmtm) REVERT: A 110 ASP cc_start: 0.7720 (m-30) cc_final: 0.7487 (m-30) REVERT: A 228 MET cc_start: 0.5302 (mtm) cc_final: 0.5066 (mtm) REVERT: A 353 GLU cc_start: 0.7462 (tp30) cc_final: 0.7218 (tp30) REVERT: A 421 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6945 (mm-30) REVERT: A 426 GLU cc_start: 0.7836 (tt0) cc_final: 0.7567 (tt0) REVERT: A 534 LYS cc_start: 0.6903 (mmtp) cc_final: 0.6336 (tptp) REVERT: A 541 ASN cc_start: 0.7601 (t0) cc_final: 0.6917 (p0) REVERT: A 597 GLU cc_start: 0.7843 (pt0) cc_final: 0.6720 (tp30) REVERT: A 617 GLN cc_start: 0.7988 (mt0) cc_final: 0.6674 (pp30) REVERT: A 618 GLN cc_start: 0.8141 (mt0) cc_final: 0.7443 (mm110) REVERT: A 625 LEU cc_start: 0.8517 (tp) cc_final: 0.8258 (tm) REVERT: A 630 ASP cc_start: 0.7547 (t70) cc_final: 0.6680 (m-30) REVERT: A 741 ASP cc_start: 0.7023 (p0) cc_final: 0.6785 (p0) REVERT: A 754 GLU cc_start: 0.7968 (pt0) cc_final: 0.7737 (tt0) REVERT: A 756 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6900 (mm-30) REVERT: A 760 ARG cc_start: 0.6418 (mtp180) cc_final: 0.5829 (ttt-90) REVERT: A 761 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7358 (ttp-110) REVERT: A 787 GLN cc_start: 0.7388 (tt0) cc_final: 0.7058 (tm-30) REVERT: A 811 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7901 (tttp) REVERT: A 824 GLN cc_start: 0.6718 (tt0) cc_final: 0.6079 (tp40) REVERT: A 842 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7432 (mtm-85) REVERT: A 843 GLU cc_start: 0.7223 (tp30) cc_final: 0.6525 (mp0) REVERT: A 844 MET cc_start: 0.7993 (mtp) cc_final: 0.7743 (mtm) outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 1.4298 time to fit residues: 119.0727 Evaluate side-chains 81 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.0570 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 815 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5882 Z= 0.156 Angle : 0.765 15.829 7995 Z= 0.335 Chirality : 0.042 0.131 872 Planarity : 0.004 0.028 1019 Dihedral : 11.059 77.531 846 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.67 % Allowed : 6.72 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.91 (0.31), residues: 707 helix: 1.41 (0.32), residues: 276 sheet: -0.03 (0.43), residues: 116 loop : 0.28 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 130 HIS 0.006 0.001 HIS A 98 PHE 0.014 0.002 PHE A 444 TYR 0.017 0.002 TYR A 399 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.552 Fit side-chains REVERT: A 70 GLU cc_start: 0.7652 (pm20) cc_final: 0.7111 (pp20) REVERT: A 72 ASP cc_start: 0.7361 (p0) cc_final: 0.6879 (m-30) REVERT: A 73 GLU cc_start: 0.7488 (pp20) cc_final: 0.7074 (pm20) REVERT: A 91 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6859 (mtp-110) REVERT: A 100 LYS cc_start: 0.7439 (mmtm) cc_final: 0.6975 (mmtm) REVERT: A 110 ASP cc_start: 0.7666 (m-30) cc_final: 0.7433 (m-30) REVERT: A 353 GLU cc_start: 0.7406 (tp30) cc_final: 0.7103 (tp30) REVERT: A 421 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6948 (mm-30) REVERT: A 426 GLU cc_start: 0.7861 (tt0) cc_final: 0.7592 (tt0) REVERT: A 534 LYS cc_start: 0.6860 (mmtp) cc_final: 0.6321 (tptp) REVERT: A 541 ASN cc_start: 0.7552 (t0) cc_final: 0.6900 (p0) REVERT: A 597 GLU cc_start: 0.7815 (pt0) cc_final: 0.6670 (tp30) REVERT: A 617 GLN cc_start: 0.7971 (mt0) cc_final: 0.6652 (pp30) REVERT: A 618 GLN cc_start: 0.8126 (mt0) cc_final: 0.7438 (mm110) REVERT: A 625 LEU cc_start: 0.8459 (tp) cc_final: 0.8223 (tm) REVERT: A 630 ASP cc_start: 0.7477 (t70) cc_final: 0.6621 (m-30) REVERT: A 741 ASP cc_start: 0.7012 (p0) cc_final: 0.6796 (p0) REVERT: A 756 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6898 (mm-30) REVERT: A 760 ARG cc_start: 0.6424 (mtp180) cc_final: 0.5854 (ttt-90) REVERT: A 761 ARG cc_start: 0.7633 (ttp-170) cc_final: 0.7352 (ttp-110) REVERT: A 787 GLN cc_start: 0.7426 (tt0) cc_final: 0.7102 (tm-30) REVERT: A 811 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7420 (tppt) REVERT: A 824 GLN cc_start: 0.6760 (tt0) cc_final: 0.6120 (tp40) REVERT: A 842 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7457 (mtm-85) REVERT: A 843 GLU cc_start: 0.7303 (tp30) cc_final: 0.6562 (mp0) REVERT: A 844 MET cc_start: 0.7976 (mtp) cc_final: 0.7725 (mtm) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 1.4659 time to fit residues: 120.5058 Evaluate side-chains 77 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5882 Z= 0.222 Angle : 0.816 15.923 7995 Z= 0.367 Chirality : 0.045 0.158 872 Planarity : 0.004 0.029 1019 Dihedral : 11.147 77.081 846 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.18 % Allowed : 6.89 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.78 (0.31), residues: 707 helix: 1.25 (0.32), residues: 276 sheet: -0.14 (0.42), residues: 118 loop : 0.29 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 130 HIS 0.008 0.002 HIS A 98 PHE 0.017 0.002 PHE A 590 TYR 0.020 0.002 TYR A 490 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.627 Fit side-chains REVERT: A 70 GLU cc_start: 0.7668 (pm20) cc_final: 0.7122 (pp20) REVERT: A 72 ASP cc_start: 0.7404 (p0) cc_final: 0.6910 (m-30) REVERT: A 73 GLU cc_start: 0.7468 (pp20) cc_final: 0.7050 (pm20) REVERT: A 91 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6835 (mtp-110) REVERT: A 100 LYS cc_start: 0.7470 (mmtm) cc_final: 0.6999 (mmtm) REVERT: A 110 ASP cc_start: 0.7700 (m-30) cc_final: 0.7470 (m-30) REVERT: A 353 GLU cc_start: 0.7466 (tp30) cc_final: 0.7208 (tp30) REVERT: A 421 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6972 (mm-30) REVERT: A 426 GLU cc_start: 0.7826 (tt0) cc_final: 0.7553 (tt0) REVERT: A 534 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6261 (tptp) REVERT: A 541 ASN cc_start: 0.7558 (t0) cc_final: 0.6917 (p0) REVERT: A 597 GLU cc_start: 0.7812 (pt0) cc_final: 0.6688 (tp30) REVERT: A 617 GLN cc_start: 0.7973 (mt0) cc_final: 0.6646 (pp30) REVERT: A 618 GLN cc_start: 0.8132 (mt0) cc_final: 0.7402 (mm110) REVERT: A 625 LEU cc_start: 0.8522 (tp) cc_final: 0.8271 (tm) REVERT: A 630 ASP cc_start: 0.7386 (t70) cc_final: 0.6549 (m-30) REVERT: A 741 ASP cc_start: 0.6954 (p0) cc_final: 0.6721 (p0) REVERT: A 756 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6946 (mm-30) REVERT: A 760 ARG cc_start: 0.6399 (mtp180) cc_final: 0.5842 (ttt-90) REVERT: A 761 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7370 (ttp-110) REVERT: A 787 GLN cc_start: 0.7445 (tt0) cc_final: 0.7079 (tm-30) REVERT: A 811 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7898 (tttp) REVERT: A 824 GLN cc_start: 0.6705 (tt0) cc_final: 0.6063 (tp40) REVERT: A 842 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7443 (mtm-85) REVERT: A 843 GLU cc_start: 0.7309 (tp30) cc_final: 0.6567 (mp0) REVERT: A 844 MET cc_start: 0.8010 (mtp) cc_final: 0.7747 (mtm) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 1.3809 time to fit residues: 115.1091 Evaluate side-chains 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5882 Z= 0.267 Angle : 0.850 16.330 7995 Z= 0.388 Chirality : 0.047 0.166 872 Planarity : 0.005 0.031 1019 Dihedral : 11.253 75.677 846 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.01 % Allowed : 6.89 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.71 (0.31), residues: 707 helix: 1.16 (0.32), residues: 275 sheet: -0.17 (0.42), residues: 118 loop : 0.28 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 130 HIS 0.009 0.002 HIS A 98 PHE 0.019 0.002 PHE A 590 TYR 0.022 0.003 TYR A 490 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.653 Fit side-chains REVERT: A 70 GLU cc_start: 0.7588 (pm20) cc_final: 0.7056 (pp20) REVERT: A 72 ASP cc_start: 0.7381 (p0) cc_final: 0.6900 (m-30) REVERT: A 73 GLU cc_start: 0.7442 (pp20) cc_final: 0.7035 (pm20) REVERT: A 91 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6847 (mtp-110) REVERT: A 100 LYS cc_start: 0.7467 (mmtm) cc_final: 0.6997 (mmtm) REVERT: A 110 ASP cc_start: 0.7726 (m-30) cc_final: 0.7504 (m-30) REVERT: A 228 MET cc_start: 0.5213 (mtm) cc_final: 0.4981 (mtm) REVERT: A 421 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6974 (mm-30) REVERT: A 426 GLU cc_start: 0.7841 (tt0) cc_final: 0.7575 (tt0) REVERT: A 534 LYS cc_start: 0.6899 (mmtp) cc_final: 0.6271 (tptp) REVERT: A 541 ASN cc_start: 0.7557 (t0) cc_final: 0.6921 (p0) REVERT: A 597 GLU cc_start: 0.7865 (pt0) cc_final: 0.6741 (tp30) REVERT: A 617 GLN cc_start: 0.7982 (mt0) cc_final: 0.6658 (pp30) REVERT: A 625 LEU cc_start: 0.8531 (tp) cc_final: 0.8285 (tm) REVERT: A 741 ASP cc_start: 0.6964 (p0) cc_final: 0.6729 (p0) REVERT: A 756 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6966 (mm-30) REVERT: A 760 ARG cc_start: 0.6379 (mtp180) cc_final: 0.5739 (ttm-80) REVERT: A 761 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7444 (ttp-110) REVERT: A 787 GLN cc_start: 0.7380 (tt0) cc_final: 0.7022 (tm-30) REVERT: A 811 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7865 (tttp) REVERT: A 842 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7435 (mtm-85) REVERT: A 843 GLU cc_start: 0.7327 (tp30) cc_final: 0.6589 (mp0) REVERT: A 844 MET cc_start: 0.7996 (mtp) cc_final: 0.7733 (mtm) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 1.4412 time to fit residues: 115.8392 Evaluate side-chains 75 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 chunk 37 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5882 Z= 0.135 Angle : 0.748 15.095 7995 Z= 0.324 Chirality : 0.041 0.131 872 Planarity : 0.004 0.027 1019 Dihedral : 10.986 79.439 846 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.84 % Allowed : 7.39 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.97 (0.31), residues: 707 helix: 1.47 (0.32), residues: 275 sheet: -0.13 (0.42), residues: 118 loop : 0.37 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 502 HIS 0.005 0.001 HIS A 98 PHE 0.011 0.001 PHE A 444 TYR 0.017 0.001 TYR A 399 ARG 0.006 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.850 Fit side-chains REVERT: A 70 GLU cc_start: 0.7537 (pm20) cc_final: 0.6992 (pp20) REVERT: A 72 ASP cc_start: 0.7330 (p0) cc_final: 0.6836 (m-30) REVERT: A 73 GLU cc_start: 0.7546 (pp20) cc_final: 0.7141 (pm20) REVERT: A 91 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6845 (mtp-110) REVERT: A 100 LYS cc_start: 0.7442 (mmtm) cc_final: 0.6976 (mmtm) REVERT: A 110 ASP cc_start: 0.7653 (m-30) cc_final: 0.7427 (m-30) REVERT: A 228 MET cc_start: 0.5171 (mtm) cc_final: 0.4949 (mtm) REVERT: A 353 GLU cc_start: 0.7443 (tp30) cc_final: 0.7167 (tp30) REVERT: A 421 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6990 (mm-30) REVERT: A 426 GLU cc_start: 0.7866 (tt0) cc_final: 0.7586 (tt0) REVERT: A 534 LYS cc_start: 0.6830 (mmtp) cc_final: 0.6230 (tptp) REVERT: A 541 ASN cc_start: 0.7527 (t0) cc_final: 0.6965 (p0) REVERT: A 597 GLU cc_start: 0.7768 (pt0) cc_final: 0.6642 (tp30) REVERT: A 617 GLN cc_start: 0.7960 (mt0) cc_final: 0.6664 (pp30) REVERT: A 618 GLN cc_start: 0.8122 (mt0) cc_final: 0.7455 (mm110) REVERT: A 625 LEU cc_start: 0.8461 (tp) cc_final: 0.8235 (tm) REVERT: A 741 ASP cc_start: 0.6997 (p0) cc_final: 0.6776 (p0) REVERT: A 756 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6890 (mm-30) REVERT: A 760 ARG cc_start: 0.6354 (mtp180) cc_final: 0.5864 (ttt-90) REVERT: A 761 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7356 (ttp-110) REVERT: A 787 GLN cc_start: 0.7408 (tt0) cc_final: 0.7046 (tm-30) REVERT: A 811 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7405 (tppt) REVERT: A 842 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7420 (mtm-85) REVERT: A 843 GLU cc_start: 0.7363 (tp30) cc_final: 0.6646 (mp0) REVERT: A 844 MET cc_start: 0.7964 (mtp) cc_final: 0.7725 (mtm) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 1.4370 time to fit residues: 115.8190 Evaluate side-chains 76 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 62 optimal weight: 0.1980 chunk 37 optimal weight: 0.1980 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5882 Z= 0.130 Angle : 0.742 14.767 7995 Z= 0.318 Chirality : 0.041 0.126 872 Planarity : 0.004 0.027 1019 Dihedral : 10.860 81.879 846 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.01 % Allowed : 7.73 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.32), residues: 707 helix: 1.57 (0.33), residues: 276 sheet: -0.16 (0.42), residues: 118 loop : 0.51 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.004 0.001 HIS A 98 PHE 0.011 0.001 PHE A 444 TYR 0.016 0.001 TYR A 399 ARG 0.009 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.548 Fit side-chains REVERT: A 70 GLU cc_start: 0.7529 (pm20) cc_final: 0.6983 (pp20) REVERT: A 72 ASP cc_start: 0.7293 (p0) cc_final: 0.6805 (m-30) REVERT: A 73 GLU cc_start: 0.7542 (pp20) cc_final: 0.7139 (pm20) REVERT: A 91 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6856 (mtp-110) REVERT: A 100 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6921 (mmtm) REVERT: A 110 ASP cc_start: 0.7622 (m-30) cc_final: 0.7410 (m-30) REVERT: A 228 MET cc_start: 0.5170 (mtm) cc_final: 0.4559 (mtp) REVERT: A 353 GLU cc_start: 0.7383 (tp30) cc_final: 0.7089 (tp30) REVERT: A 421 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6992 (mm-30) REVERT: A 426 GLU cc_start: 0.7850 (tt0) cc_final: 0.7570 (tt0) REVERT: A 534 LYS cc_start: 0.6840 (mmtp) cc_final: 0.6243 (tptp) REVERT: A 541 ASN cc_start: 0.7447 (t0) cc_final: 0.6867 (p0) REVERT: A 597 GLU cc_start: 0.7773 (pt0) cc_final: 0.6643 (tp30) REVERT: A 617 GLN cc_start: 0.7951 (mt0) cc_final: 0.6679 (pp30) REVERT: A 618 GLN cc_start: 0.8080 (mt0) cc_final: 0.7411 (mm110) REVERT: A 625 LEU cc_start: 0.8466 (tp) cc_final: 0.8226 (tm) REVERT: A 630 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6442 (m-30) REVERT: A 741 ASP cc_start: 0.7008 (p0) cc_final: 0.6793 (p0) REVERT: A 756 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6881 (mm-30) REVERT: A 760 ARG cc_start: 0.6363 (mtp180) cc_final: 0.5888 (ttt-90) REVERT: A 761 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7373 (ttp-110) REVERT: A 787 GLN cc_start: 0.7442 (tt0) cc_final: 0.7086 (tm-30) REVERT: A 788 ILE cc_start: 0.7363 (mt) cc_final: 0.7135 (mt) REVERT: A 811 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7755 (tppt) REVERT: A 842 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7418 (mtm-85) REVERT: A 843 GLU cc_start: 0.7295 (tp30) cc_final: 0.6566 (mp0) REVERT: A 844 MET cc_start: 0.7960 (mtp) cc_final: 0.7701 (mtm) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 1.3415 time to fit residues: 109.0883 Evaluate side-chains 76 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5882 Z= 0.205 Angle : 0.798 15.344 7995 Z= 0.354 Chirality : 0.044 0.161 872 Planarity : 0.004 0.030 1019 Dihedral : 10.981 78.909 846 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.18 % Allowed : 7.73 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.95 (0.31), residues: 707 helix: 1.38 (0.32), residues: 275 sheet: -0.08 (0.42), residues: 118 loop : 0.41 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 130 HIS 0.007 0.001 HIS A 729 PHE 0.016 0.002 PHE A 590 TYR 0.019 0.002 TYR A 490 ARG 0.008 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.594 Fit side-chains REVERT: A 70 GLU cc_start: 0.7592 (pm20) cc_final: 0.7057 (pp20) REVERT: A 72 ASP cc_start: 0.7352 (p0) cc_final: 0.6897 (m-30) REVERT: A 73 GLU cc_start: 0.7518 (pp20) cc_final: 0.7111 (pm20) REVERT: A 100 LYS cc_start: 0.7455 (mmtm) cc_final: 0.6995 (mmtm) REVERT: A 110 ASP cc_start: 0.7673 (m-30) cc_final: 0.7458 (m-30) REVERT: A 353 GLU cc_start: 0.7470 (tp30) cc_final: 0.7238 (tp30) REVERT: A 421 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6967 (mm-30) REVERT: A 426 GLU cc_start: 0.7832 (tt0) cc_final: 0.7549 (tt0) REVERT: A 529 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7322 (mp) REVERT: A 534 LYS cc_start: 0.6837 (mmtp) cc_final: 0.6240 (tptp) REVERT: A 541 ASN cc_start: 0.7452 (t0) cc_final: 0.6875 (p0) REVERT: A 597 GLU cc_start: 0.7805 (pt0) cc_final: 0.6673 (tp30) REVERT: A 617 GLN cc_start: 0.7965 (mt0) cc_final: 0.6688 (pp30) REVERT: A 618 GLN cc_start: 0.8142 (mt0) cc_final: 0.7424 (mm110) REVERT: A 625 LEU cc_start: 0.8512 (tp) cc_final: 0.8266 (tm) REVERT: A 741 ASP cc_start: 0.6998 (p0) cc_final: 0.6763 (p0) REVERT: A 756 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6944 (mm-30) REVERT: A 760 ARG cc_start: 0.6378 (mtp180) cc_final: 0.5895 (ttt-90) REVERT: A 761 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7410 (ttp-110) REVERT: A 787 GLN cc_start: 0.7427 (tt0) cc_final: 0.7082 (tm-30) REVERT: A 811 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7948 (tttp) REVERT: A 842 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7420 (mtm-85) REVERT: A 843 GLU cc_start: 0.7290 (tp30) cc_final: 0.6556 (mp0) REVERT: A 844 MET cc_start: 0.8007 (mtp) cc_final: 0.7748 (mtm) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 1.3857 time to fit residues: 107.0531 Evaluate side-chains 75 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5882 Z= 0.153 Angle : 0.761 15.009 7995 Z= 0.331 Chirality : 0.042 0.143 872 Planarity : 0.004 0.030 1019 Dihedral : 10.889 80.065 846 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.01 % Allowed : 7.90 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 707 helix: 1.47 (0.32), residues: 275 sheet: -0.07 (0.42), residues: 118 loop : 0.44 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 502 HIS 0.005 0.001 HIS A 98 PHE 0.011 0.001 PHE A 444 TYR 0.017 0.002 TYR A 399 ARG 0.008 0.001 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.661 Fit side-chains REVERT: A 70 GLU cc_start: 0.7538 (pm20) cc_final: 0.6982 (pp20) REVERT: A 72 ASP cc_start: 0.7322 (p0) cc_final: 0.6852 (m-30) REVERT: A 73 GLU cc_start: 0.7536 (pp20) cc_final: 0.7135 (pm20) REVERT: A 100 LYS cc_start: 0.7432 (mmtm) cc_final: 0.6965 (mmtm) REVERT: A 110 ASP cc_start: 0.7648 (m-30) cc_final: 0.7437 (m-30) REVERT: A 353 GLU cc_start: 0.7446 (tp30) cc_final: 0.7197 (tp30) REVERT: A 421 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6995 (mm-30) REVERT: A 426 GLU cc_start: 0.7870 (tt0) cc_final: 0.7592 (tt0) REVERT: A 534 LYS cc_start: 0.6835 (mmtp) cc_final: 0.6247 (tptp) REVERT: A 541 ASN cc_start: 0.7442 (t0) cc_final: 0.6873 (p0) REVERT: A 597 GLU cc_start: 0.7793 (pt0) cc_final: 0.6661 (tp30) REVERT: A 617 GLN cc_start: 0.7951 (mt0) cc_final: 0.6685 (pp30) REVERT: A 618 GLN cc_start: 0.8131 (mt0) cc_final: 0.7468 (mm110) REVERT: A 625 LEU cc_start: 0.8475 (tp) cc_final: 0.8237 (tm) REVERT: A 741 ASP cc_start: 0.6987 (p0) cc_final: 0.6768 (p0) REVERT: A 756 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6929 (mm-30) REVERT: A 760 ARG cc_start: 0.6353 (mtp180) cc_final: 0.5892 (ttt-90) REVERT: A 761 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7364 (ttp-110) REVERT: A 787 GLN cc_start: 0.7436 (tt0) cc_final: 0.7077 (tm-30) REVERT: A 811 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7428 (tppt) REVERT: A 842 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7419 (mtm-85) REVERT: A 843 GLU cc_start: 0.7298 (tp30) cc_final: 0.6582 (mp0) REVERT: A 844 MET cc_start: 0.7963 (mtp) cc_final: 0.7709 (mtm) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 1.4314 time to fit residues: 108.8545 Evaluate side-chains 74 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165104 restraints weight = 8829.699| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 0.91 r_work: 0.3594 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5882 Z= 0.179 Angle : 0.781 15.153 7995 Z= 0.344 Chirality : 0.043 0.149 872 Planarity : 0.004 0.031 1019 Dihedral : 10.909 78.964 846 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.84 % Allowed : 7.90 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.98 (0.31), residues: 707 helix: 1.41 (0.32), residues: 275 sheet: -0.06 (0.42), residues: 118 loop : 0.42 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 502 HIS 0.006 0.001 HIS A 729 PHE 0.014 0.002 PHE A 590 TYR 0.018 0.002 TYR A 399 ARG 0.008 0.001 ARG A 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.29 seconds wall clock time: 52 minutes 0.95 seconds (3120.95 seconds total)