Starting phenix.real_space_refine on Sun Apr 7 05:05:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jul_36661/04_2024/8jul_36661_updated.pdb" } resolution = 2.92 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= 0.014 sd= 0.127 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 Zn 2 6.06 5 P 2 5.49 5 S 52 5.16 5 C 6338 2.51 5 N 1564 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 776": "NH1" <-> "NH2" Residue "B ARG 820": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4807 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4807 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'PX2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'PX2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.58 Number of scatterers: 9690 At special positions: 0 Unit cell: (73.83, 90.95, 124.12, 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) Zn 2 29.99 S 52 16.00 P 2 15.00 O 1732 8.00 N 1564 7.00 C 6338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.05 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 795 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 791 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 42.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 303 through 330 removed outlier: 4.582A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 496 through 527 removed outlier: 4.563A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 564 Processing helix chain 'A' and resid 574 through 592 removed outlier: 4.073A pdb=" N THR A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 4.512A pdb=" N VAL A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 651 removed outlier: 3.538A pdb=" N PHE A 632 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 658 No H-bonds generated for 'chain 'A' and resid 655 through 658' Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 709 through 734 Processing helix chain 'A' and resid 741 through 762 removed outlier: 4.058A pdb=" N PHE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.699A pdb=" N GLU A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 810 removed outlier: 3.814A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 330 removed outlier: 4.583A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 496 through 527 removed outlier: 4.564A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE B 509 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 564 Processing helix chain 'B' and resid 574 through 592 removed outlier: 4.074A pdb=" N THR B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 4.512A pdb=" N VAL B 619 " --> pdb=" O THR B 615 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 651 removed outlier: 3.537A pdb=" N PHE B 632 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 650 " --> pdb=" O GLN B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 658 No H-bonds generated for 'chain 'B' and resid 655 through 658' Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 709 through 734 Processing helix chain 'B' and resid 741 through 762 removed outlier: 4.059A pdb=" N PHE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 777 removed outlier: 3.699A pdb=" N GLU B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 810 removed outlier: 3.814A pdb=" N ALA B 799 " --> pdb=" O HIS B 795 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 44 through 46 removed outlier: 4.519A pdb=" N ASN A 67 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= D, first strand: chain 'A' and resid 176 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.753A pdb=" N VAL A 236 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 removed outlier: 4.519A pdb=" N ASN B 67 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 52 through 55 Processing sheet with id= H, first strand: chain 'B' and resid 110 through 114 Processing sheet with id= I, first strand: chain 'B' and resid 176 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.753A pdb=" N VAL B 236 " --> pdb=" O VAL B 217 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1569 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: 2.55 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1532 1.29 - 1.43: 2754 1.43 - 1.56: 5543 1.56 - 1.70: 5 1.70 - 1.84: 78 Bond restraints: 9912 Sorted by residual: bond pdb=" CA MET A 221 " pdb=" C MET A 221 " ideal model delta sigma weight residual 1.521 1.420 0.102 1.28e-02 6.10e+03 6.31e+01 bond pdb=" N GLU A 769 " pdb=" CA GLU A 769 " ideal model delta sigma weight residual 1.459 1.371 0.088 1.23e-02 6.61e+03 5.09e+01 bond pdb=" O2 PX2 B 902 " pdb=" P1 PX2 B 902 " ideal model delta sigma weight residual 1.510 1.646 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" CA CYS A 222 " pdb=" C CYS A 222 " ideal model delta sigma weight residual 1.524 1.444 0.079 1.26e-02 6.30e+03 3.97e+01 bond pdb=" O2 PX2 A 902 " pdb=" P1 PX2 A 902 " ideal model delta sigma weight residual 1.510 1.631 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 9907 not shown) Histogram of bond angle deviations from ideal: 77.93 - 91.54: 6 91.54 - 105.14: 170 105.14 - 118.75: 7652 118.75 - 132.36: 5622 132.36 - 145.97: 18 Bond angle restraints: 13468 Sorted by residual: angle pdb=" N GLY B 272 " pdb=" CA GLY B 272 " pdb=" C GLY B 272 " ideal model delta sigma weight residual 114.16 145.23 -31.07 1.21e+00 6.83e-01 6.59e+02 angle pdb=" N GLY A 272 " pdb=" CA GLY A 272 " pdb=" C GLY A 272 " ideal model delta sigma weight residual 115.73 145.97 -30.24 1.59e+00 3.96e-01 3.62e+02 angle pdb=" N PHE B 700 " pdb=" CA PHE B 700 " pdb=" C PHE B 700 " ideal model delta sigma weight residual 112.12 134.83 -22.71 1.34e+00 5.57e-01 2.87e+02 angle pdb=" C ARG A 705 " pdb=" CA ARG A 705 " pdb=" CB ARG A 705 " ideal model delta sigma weight residual 110.10 77.93 32.17 1.90e+00 2.77e-01 2.87e+02 angle pdb=" N CYS B 271 " pdb=" CA CYS B 271 " pdb=" C CYS B 271 " ideal model delta sigma weight residual 109.52 85.56 23.96 1.55e+00 4.16e-01 2.39e+02 ... (remaining 13463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.86: 5338 19.86 - 39.72: 408 39.72 - 59.59: 53 59.59 - 79.45: 13 79.45 - 99.31: 8 Dihedral angle restraints: 5820 sinusoidal: 2140 harmonic: 3680 Sorted by residual: dihedral pdb=" CA VAL B 108 " pdb=" C VAL B 108 " pdb=" N PRO B 109 " pdb=" CA PRO B 109 " ideal model delta harmonic sigma weight residual 180.00 80.69 99.31 0 5.00e+00 4.00e-02 3.94e+02 dihedral pdb=" CA VAL A 108 " pdb=" C VAL A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta harmonic sigma weight residual 180.00 80.70 99.30 0 5.00e+00 4.00e-02 3.94e+02 dihedral pdb=" C ARG A 705 " pdb=" N ARG A 705 " pdb=" CA ARG A 705 " pdb=" CB ARG A 705 " ideal model delta harmonic sigma weight residual -122.60 -86.47 -36.13 0 2.50e+00 1.60e-01 2.09e+02 ... (remaining 5817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 1533 0.317 - 0.634: 7 0.634 - 0.951: 1 0.951 - 1.267: 0 1.267 - 1.584: 1 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA CYS A 222 " pdb=" N CYS A 222 " pdb=" C CYS A 222 " pdb=" CB CYS A 222 " both_signs ideal model delta sigma weight residual False 2.51 0.93 1.58 2.00e-01 2.50e+01 6.27e+01 chirality pdb=" CA LEU A 699 " pdb=" N LEU A 699 " pdb=" C LEU A 699 " pdb=" CB LEU A 699 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" CA ARG A 707 " pdb=" N ARG A 707 " pdb=" C ARG A 707 " pdb=" CB ARG A 707 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 1539 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 108 " -0.115 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO B 109 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 108 " 0.091 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO A 109 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 108 " -0.025 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C VAL A 108 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 108 " -0.031 2.00e-02 2.50e+03 pdb=" N PRO A 109 " -0.030 2.00e-02 2.50e+03 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 56 2.45 - 3.06: 6396 3.06 - 3.67: 14287 3.67 - 4.29: 22010 4.29 - 4.90: 37000 Nonbonded interactions: 79749 Sorted by model distance: nonbonded pdb=" O ARG A 705 " pdb=" CB ARG A 705 " model vdw 1.832 2.752 nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1001 " model vdw 1.987 2.230 nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1001 " model vdw 1.988 2.230 nonbonded pdb=" N CYS B 271 " pdb=" O CYS B 271 " model vdw 2.090 2.496 nonbonded pdb=" OG SER A 105 " pdb=" OG SER B 105 " model vdw 2.116 2.440 ... (remaining 79744 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: 0.680 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: 2.300 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.690 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.010 0.136 9912 Z= 0.659 Angle : 1.316 32.171 13468 Z= 0.769 Chirality : 0.079 1.584 1542 Planarity : 0.008 0.175 1694 Dihedral : 14.582 99.308 3412 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.09 (0.21), residues: 1218 helix: -1.68 (0.19), residues: 542 sheet: -0.86 (0.28), residues: 292 loop : -3.33 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 768 HIS 0.007 0.001 HIS B 487 PHE 0.023 0.002 PHE A 803 TYR 0.012 0.002 TYR A 759 ARG 0.005 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.197 Fit side-chains REVERT: A 519 ASP cc_start: 0.7685 (t70) cc_final: 0.7385 (OUTLIER) REVERT: A 524 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7406 (ttp-170) REVERT: A 578 MET cc_start: 0.7884 (mmt) cc_final: 0.7048 (mmt) REVERT: A 711 SER cc_start: 0.8473 (t) cc_final: 0.8208 (p) REVERT: A 717 PHE cc_start: 0.8254 (t80) cc_final: 0.7853 (t80) REVERT: B 118 ARG cc_start: 0.7433 (ttm170) cc_final: 0.7210 (ttm-80) REVERT: B 519 ASP cc_start: 0.7685 (t70) cc_final: 0.7391 (OUTLIER) REVERT: B 524 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7413 (ttp-170) REVERT: B 578 MET cc_start: 0.7874 (mmt) cc_final: 0.6959 (mmt) REVERT: B 711 SER cc_start: 0.8529 (t) cc_final: 0.8278 (p) REVERT: B 717 PHE cc_start: 0.8220 (t80) cc_final: 0.7849 (t80) outliers start: 0 outliers final: 2 residues processed: 154 average time/residue: 1.0295 time to fit residues: 172.7024 Evaluate side-chains 102 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 71 GLN A 83 ASN A 113 GLN A 142 GLN A 158 GLN A 218 GLN A 229 HIS A 467 GLN A 763 GLN A 779 ASN B 62 ASN B 71 GLN B 83 ASN B 113 GLN B 142 GLN B 158 GLN B 170 GLN B 229 HIS B 467 GLN B 763 GLN B 779 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9912 Z= 0.196 Angle : 0.592 8.572 13468 Z= 0.316 Chirality : 0.043 0.185 1542 Planarity : 0.006 0.127 1694 Dihedral : 8.677 97.860 1380 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 2.13 % Allowed : 10.57 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.37 (0.23), residues: 1218 helix: 0.21 (0.21), residues: 538 sheet: -0.30 (0.28), residues: 286 loop : -2.92 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.006 0.001 HIS B 487 PHE 0.025 0.001 PHE B 709 TYR 0.015 0.001 TYR A 712 ARG 0.002 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.152 Fit side-chains REVERT: A 221 MET cc_start: 0.7412 (tpp) cc_final: 0.7190 (mmt) REVERT: A 519 ASP cc_start: 0.7504 (t70) cc_final: 0.7181 (t0) REVERT: A 524 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7243 (ttp-170) REVERT: A 570 ASN cc_start: 0.7952 (t0) cc_final: 0.7681 (t160) REVERT: A 578 MET cc_start: 0.7718 (mmt) cc_final: 0.6798 (mmt) REVERT: A 711 SER cc_start: 0.8475 (t) cc_final: 0.8214 (p) REVERT: A 717 PHE cc_start: 0.7968 (t80) cc_final: 0.7682 (t80) REVERT: A 753 MET cc_start: 0.7565 (mmt) cc_final: 0.7285 (mmt) REVERT: B 519 ASP cc_start: 0.7518 (t70) cc_final: 0.7194 (t0) REVERT: B 524 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7272 (ttp-170) REVERT: B 570 ASN cc_start: 0.7941 (t0) cc_final: 0.7682 (t160) REVERT: B 578 MET cc_start: 0.7724 (mmt) cc_final: 0.6807 (mmt) REVERT: B 711 SER cc_start: 0.8517 (t) cc_final: 0.8290 (p) REVERT: B 717 PHE cc_start: 0.7996 (t80) cc_final: 0.7706 (t80) REVERT: B 753 MET cc_start: 0.7552 (mmt) cc_final: 0.7263 (mmt) outliers start: 21 outliers final: 2 residues processed: 147 average time/residue: 1.0219 time to fit residues: 165.1598 Evaluate side-chains 115 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain B residue 90 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 143 GLN A 288 GLN B 142 GLN B 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9912 Z= 0.347 Angle : 0.640 9.018 13468 Z= 0.340 Chirality : 0.046 0.215 1542 Planarity : 0.007 0.132 1694 Dihedral : 8.534 100.775 1380 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.47 % Allowed : 12.50 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.82 (0.24), residues: 1218 helix: 0.77 (0.22), residues: 540 sheet: -0.03 (0.28), residues: 286 loop : -2.85 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 106 HIS 0.007 0.001 HIS A 487 PHE 0.017 0.002 PHE B 803 TYR 0.013 0.002 TYR A 759 ARG 0.003 0.000 ARG B 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.088 Fit side-chains REVERT: A 519 ASP cc_start: 0.7576 (t70) cc_final: 0.7258 (t0) REVERT: A 524 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7376 (ttp-170) REVERT: A 578 MET cc_start: 0.7798 (mmt) cc_final: 0.7041 (mmt) REVERT: A 711 SER cc_start: 0.8507 (t) cc_final: 0.8224 (p) REVERT: A 717 PHE cc_start: 0.7987 (t80) cc_final: 0.7698 (t80) REVERT: B 221 MET cc_start: 0.7479 (mmt) cc_final: 0.7271 (mmt) REVERT: B 519 ASP cc_start: 0.7585 (t70) cc_final: 0.7271 (t0) REVERT: B 524 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7320 (ttp-170) REVERT: B 572 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: B 578 MET cc_start: 0.7820 (mmt) cc_final: 0.7048 (mmt) REVERT: B 711 SER cc_start: 0.8494 (t) cc_final: 0.8182 (p) REVERT: B 717 PHE cc_start: 0.8014 (t80) cc_final: 0.7720 (t80) outliers start: 44 outliers final: 19 residues processed: 146 average time/residue: 0.9235 time to fit residues: 148.7332 Evaluate side-chains 132 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 779 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 288 GLN B 142 GLN B 143 GLN B 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9912 Z= 0.206 Angle : 0.564 8.672 13468 Z= 0.299 Chirality : 0.043 0.150 1542 Planarity : 0.006 0.116 1694 Dihedral : 7.960 96.936 1380 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.57 % Allowed : 15.04 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.32 (0.24), residues: 1218 helix: 1.28 (0.22), residues: 540 sheet: 0.13 (0.28), residues: 286 loop : -2.68 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.005 0.001 HIS A 487 PHE 0.016 0.001 PHE B 709 TYR 0.012 0.001 TYR B 579 ARG 0.002 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 124 time to evaluate : 1.064 Fit side-chains REVERT: A 519 ASP cc_start: 0.7520 (t70) cc_final: 0.7215 (t0) REVERT: A 578 MET cc_start: 0.7615 (mmt) cc_final: 0.6748 (mmt) REVERT: A 711 SER cc_start: 0.8473 (t) cc_final: 0.8174 (p) REVERT: A 717 PHE cc_start: 0.7854 (t80) cc_final: 0.7619 (t80) REVERT: A 753 MET cc_start: 0.7563 (mmt) cc_final: 0.7353 (mmt) REVERT: B 519 ASP cc_start: 0.7533 (t70) cc_final: 0.7229 (t0) REVERT: B 524 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7337 (ttp-170) REVERT: B 553 MET cc_start: 0.8806 (mtp) cc_final: 0.8587 (mtm) REVERT: B 578 MET cc_start: 0.7642 (mmt) cc_final: 0.6778 (mmt) REVERT: B 711 SER cc_start: 0.8460 (t) cc_final: 0.8137 (p) REVERT: B 717 PHE cc_start: 0.7866 (t80) cc_final: 0.7611 (t80) REVERT: B 730 ILE cc_start: 0.8628 (mm) cc_final: 0.8425 (mm) REVERT: B 753 MET cc_start: 0.7568 (mmt) cc_final: 0.7358 (mmt) outliers start: 45 outliers final: 23 residues processed: 156 average time/residue: 0.8063 time to fit residues: 139.6728 Evaluate side-chains 134 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 288 GLN B 142 GLN B 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9912 Z= 0.344 Angle : 0.637 9.563 13468 Z= 0.334 Chirality : 0.046 0.173 1542 Planarity : 0.007 0.134 1694 Dihedral : 8.141 100.552 1380 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.98 % Allowed : 15.96 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.31 (0.24), residues: 1218 helix: 1.27 (0.22), residues: 540 sheet: 0.20 (0.28), residues: 292 loop : -2.74 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 106 HIS 0.005 0.001 HIS B 487 PHE 0.018 0.002 PHE B 276 TYR 0.012 0.002 TYR B 759 ARG 0.003 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 119 time to evaluate : 1.247 Fit side-chains REVERT: A 44 ARG cc_start: 0.7082 (ptp-170) cc_final: 0.6707 (ptp-170) REVERT: A 218 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: A 519 ASP cc_start: 0.7588 (t70) cc_final: 0.7303 (t0) REVERT: A 578 MET cc_start: 0.7796 (mmp) cc_final: 0.7069 (mmt) REVERT: A 711 SER cc_start: 0.8526 (t) cc_final: 0.7923 (m) REVERT: A 717 PHE cc_start: 0.7989 (t80) cc_final: 0.7708 (t80) REVERT: A 753 MET cc_start: 0.7603 (mmt) cc_final: 0.7331 (mmt) REVERT: B 218 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: B 519 ASP cc_start: 0.7642 (t70) cc_final: 0.7372 (t0) REVERT: B 578 MET cc_start: 0.7811 (mmt) cc_final: 0.7075 (mmt) REVERT: B 711 SER cc_start: 0.8508 (t) cc_final: 0.7897 (m) REVERT: B 717 PHE cc_start: 0.8009 (t80) cc_final: 0.7743 (t80) REVERT: B 730 ILE cc_start: 0.8652 (mm) cc_final: 0.8447 (mm) REVERT: B 753 MET cc_start: 0.7607 (mmt) cc_final: 0.7336 (mmt) outliers start: 49 outliers final: 30 residues processed: 153 average time/residue: 0.8899 time to fit residues: 150.0586 Evaluate side-chains 138 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 288 GLN B 142 GLN B 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9912 Z= 0.256 Angle : 0.594 8.514 13468 Z= 0.312 Chirality : 0.044 0.166 1542 Planarity : 0.006 0.125 1694 Dihedral : 7.913 98.603 1380 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.57 % Allowed : 16.36 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.11 (0.24), residues: 1218 helix: 1.45 (0.22), residues: 540 sheet: 0.29 (0.28), residues: 290 loop : -2.64 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 106 HIS 0.005 0.001 HIS A 487 PHE 0.016 0.001 PHE B 276 TYR 0.010 0.001 TYR A 759 ARG 0.002 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 1.189 Fit side-chains REVERT: A 102 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: A 519 ASP cc_start: 0.7569 (t70) cc_final: 0.7306 (t0) REVERT: A 553 MET cc_start: 0.8857 (mtp) cc_final: 0.8616 (mtm) REVERT: A 570 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 572 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: A 578 MET cc_start: 0.7723 (mmp) cc_final: 0.6912 (mmt) REVERT: A 711 SER cc_start: 0.8474 (t) cc_final: 0.7901 (m) REVERT: A 717 PHE cc_start: 0.7902 (t80) cc_final: 0.7647 (t80) REVERT: A 753 MET cc_start: 0.7607 (mmt) cc_final: 0.7378 (mmt) REVERT: B 218 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: B 519 ASP cc_start: 0.7599 (t70) cc_final: 0.7340 (t0) REVERT: B 578 MET cc_start: 0.7769 (mmp) cc_final: 0.6969 (mmt) REVERT: B 711 SER cc_start: 0.8535 (t) cc_final: 0.7946 (m) REVERT: B 717 PHE cc_start: 0.7920 (t80) cc_final: 0.7670 (t80) REVERT: B 753 MET cc_start: 0.7611 (mmt) cc_final: 0.7381 (mmt) outliers start: 45 outliers final: 32 residues processed: 145 average time/residue: 0.8152 time to fit residues: 131.7344 Evaluate side-chains 144 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 288 GLN B 142 GLN B 288 GLN B 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9912 Z= 0.165 Angle : 0.561 8.737 13468 Z= 0.291 Chirality : 0.042 0.145 1542 Planarity : 0.006 0.127 1694 Dihedral : 7.273 95.105 1380 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.27 % Allowed : 17.68 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 0.15 (0.24), residues: 1218 helix: 1.71 (0.22), residues: 540 sheet: 0.30 (0.29), residues: 292 loop : -2.50 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 487 PHE 0.013 0.001 PHE A 317 TYR 0.008 0.001 TYR B 759 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 1.139 Fit side-chains REVERT: A 218 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: A 519 ASP cc_start: 0.7483 (t70) cc_final: 0.7244 (t0) REVERT: A 553 MET cc_start: 0.8818 (mtp) cc_final: 0.8604 (mtm) REVERT: A 570 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 572 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: A 578 MET cc_start: 0.7579 (mmp) cc_final: 0.6634 (mmt) REVERT: A 711 SER cc_start: 0.8466 (t) cc_final: 0.8046 (m) REVERT: A 753 MET cc_start: 0.7506 (mmt) cc_final: 0.7294 (mmt) REVERT: B 519 ASP cc_start: 0.7503 (t70) cc_final: 0.7265 (t0) REVERT: B 553 MET cc_start: 0.8784 (mtp) cc_final: 0.8576 (mtm) REVERT: B 572 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 578 MET cc_start: 0.7603 (mmp) cc_final: 0.6655 (mmt) REVERT: B 711 SER cc_start: 0.8481 (t) cc_final: 0.8084 (m) REVERT: B 753 MET cc_start: 0.7515 (mmt) cc_final: 0.7306 (mmt) outliers start: 42 outliers final: 27 residues processed: 154 average time/residue: 0.8051 time to fit residues: 138.8931 Evaluate side-chains 149 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 50.0000 chunk 71 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9912 Z= 0.193 Angle : 0.572 9.295 13468 Z= 0.294 Chirality : 0.043 0.138 1542 Planarity : 0.006 0.133 1694 Dihedral : 7.192 95.793 1380 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.47 % Allowed : 18.09 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 0.30 (0.24), residues: 1218 helix: 1.80 (0.22), residues: 550 sheet: 0.32 (0.29), residues: 292 loop : -2.41 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS B 487 PHE 0.014 0.001 PHE B 276 TYR 0.016 0.001 TYR A 712 ARG 0.002 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 1.185 Fit side-chains REVERT: A 218 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: A 519 ASP cc_start: 0.7433 (t70) cc_final: 0.7204 (t0) REVERT: A 553 MET cc_start: 0.8829 (mtp) cc_final: 0.8609 (mtm) REVERT: A 570 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7676 (t0) REVERT: A 572 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 578 MET cc_start: 0.7629 (mmp) cc_final: 0.6515 (mmt) REVERT: A 711 SER cc_start: 0.8422 (t) cc_final: 0.8012 (m) REVERT: A 753 MET cc_start: 0.7524 (mmt) cc_final: 0.7317 (mmt) REVERT: B 519 ASP cc_start: 0.7446 (t70) cc_final: 0.7204 (t0) REVERT: B 553 MET cc_start: 0.8800 (mtp) cc_final: 0.8573 (mtm) REVERT: B 572 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: B 711 SER cc_start: 0.8448 (t) cc_final: 0.7957 (m) REVERT: B 753 MET cc_start: 0.7530 (mmt) cc_final: 0.7329 (mmt) outliers start: 44 outliers final: 31 residues processed: 151 average time/residue: 0.8456 time to fit residues: 141.6197 Evaluate side-chains 150 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 50.0000 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 9912 Z= 0.564 Angle : 0.766 12.844 13468 Z= 0.398 Chirality : 0.051 0.199 1542 Planarity : 0.007 0.148 1694 Dihedral : 8.043 104.239 1380 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.67 % Allowed : 17.68 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.22 (0.24), residues: 1218 helix: 1.25 (0.22), residues: 542 sheet: 0.35 (0.29), residues: 292 loop : -2.66 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 106 HIS 0.006 0.002 HIS A 487 PHE 0.021 0.002 PHE B 495 TYR 0.018 0.002 TYR A 759 ARG 0.007 0.001 ARG B 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 1.189 Fit side-chains REVERT: A 218 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: A 519 ASP cc_start: 0.7723 (t70) cc_final: 0.7507 (t0) REVERT: A 578 MET cc_start: 0.7846 (mmp) cc_final: 0.7180 (mmt) REVERT: B 102 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: B 208 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6736 (tpt) REVERT: B 218 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: B 519 ASP cc_start: 0.7731 (t70) cc_final: 0.7518 (t0) REVERT: B 555 GLU cc_start: 0.8289 (tp30) cc_final: 0.8067 (tp30) outliers start: 46 outliers final: 33 residues processed: 147 average time/residue: 0.8856 time to fit residues: 143.5125 Evaluate side-chains 145 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 78 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 570 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9912 Z= 0.174 Angle : 0.597 9.888 13468 Z= 0.306 Chirality : 0.043 0.147 1542 Planarity : 0.006 0.135 1694 Dihedral : 7.400 96.291 1380 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.46 % Allowed : 19.82 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 0.20 (0.24), residues: 1218 helix: 1.71 (0.22), residues: 550 sheet: 0.35 (0.29), residues: 292 loop : -2.56 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 487 PHE 0.015 0.001 PHE B 276 TYR 0.019 0.001 TYR A 712 ARG 0.002 0.000 ARG A 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 1.233 Fit side-chains REVERT: A 218 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: A 519 ASP cc_start: 0.7490 (t70) cc_final: 0.7262 (t0) REVERT: A 572 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: A 578 MET cc_start: 0.7594 (mmp) cc_final: 0.6671 (mmt) REVERT: A 711 SER cc_start: 0.8413 (t) cc_final: 0.7905 (m) REVERT: B 208 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6705 (tpt) REVERT: B 519 ASP cc_start: 0.7509 (t70) cc_final: 0.7278 (t0) REVERT: B 711 SER cc_start: 0.8399 (t) cc_final: 0.7767 (m) outliers start: 34 outliers final: 28 residues processed: 143 average time/residue: 0.8362 time to fit residues: 132.7302 Evaluate side-chains 148 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114519 restraints weight = 11047.755| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.02 r_work: 0.3138 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9912 Z= 0.217 Angle : 0.607 10.552 13468 Z= 0.311 Chirality : 0.043 0.152 1542 Planarity : 0.006 0.139 1694 Dihedral : 7.299 96.967 1380 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.76 % Allowed : 20.12 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 0.34 (0.24), residues: 1218 helix: 1.83 (0.22), residues: 550 sheet: 0.41 (0.29), residues: 292 loop : -2.48 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 106 HIS 0.005 0.001 HIS A 487 PHE 0.015 0.001 PHE B 276 TYR 0.019 0.001 TYR B 712 ARG 0.002 0.000 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.45 seconds wall clock time: 56 minutes 33.17 seconds (3393.17 seconds total)