Starting phenix.real_space_refine on Wed Feb 14 18:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3w_27166/02_2024/8d3w_27166_neut_updated.pdb" } resolution = 3.5 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 61 5.16 5 C 6418 2.51 5 N 1684 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 7529 Chain: "B" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2348 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 267} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 254 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 824 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 824 " occ=0.50 Time building chain proxies: 8.63, per 1000 atoms: 0.86 Number of scatterers: 10046 At special positions: 0 Unit cell: (140.4, 112.32, 127.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 3 15.00 O 1880 8.00 N 1684 7.00 C 6418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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: 3.98 Conformation dependent library (CDL) restraints added in 3.0 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 40.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.909A pdb=" N GLN A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 89 through 107 removed outlier: 4.040A pdb=" N ILE A 92 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 93 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 107 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 154 removed outlier: 3.572A pdb=" N SER A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 273 through 303 Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'A' and resid 326 through 343 Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 442 through 453 removed outlier: 6.115A pdb=" N LEU A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 501 through 507 removed outlier: 4.084A pdb=" N ASP A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.517A pdb=" N GLU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 657 through 662 removed outlier: 3.521A pdb=" N LYS A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 662' Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 709 through 717 removed outlier: 3.568A pdb=" N SER A 712 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Proline residue: A 713 - end of helix Processing helix chain 'A' and resid 730 through 734 Processing helix chain 'A' and resid 746 through 773 removed outlier: 3.862A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 794 through 801 Processing helix chain 'A' and resid 808 through 814 removed outlier: 3.619A pdb=" N TYR A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'A' and resid 847 through 865 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 877 through 880 No H-bonds generated for 'chain 'A' and resid 877 through 880' Processing helix chain 'A' and resid 898 through 926 removed outlier: 3.617A pdb=" N VAL A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 904 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 936 No H-bonds generated for 'chain 'A' and resid 934 through 936' Processing helix chain 'A' and resid 942 through 960 removed outlier: 3.569A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.617A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1001 Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'B' and resid 33 through 60 removed outlier: 3.725A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.790A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'G' and resid 37 through 57 Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.588A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.340A pdb=" N CYS A 201 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP A 204 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N CYS A 239 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 738 through 740 removed outlier: 3.620A pdb=" N ILE A 720 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 602 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER A 365 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 604 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 678 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.635A pdb=" N PHE A 383 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 547 through 550 removed outlier: 4.212A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 481 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 480 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU A 484 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYS A 466 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 510 through 513 Processing sheet with id= G, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.582A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 87 through 91 removed outlier: 8.358A pdb=" N ILE B 88 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 298 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE B 90 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU B 300 " --> pdb=" O PHE B 90 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1032 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: 2.82 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.20 - 0.53: 1 0.53 - 0.86: 0 0.86 - 1.20: 0 1.20 - 1.53: 9713 1.53 - 1.87: 541 Warning: very small bond lengths. Bond restraints: 10255 Sorted by residual: bond pdb=" CG PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 1.503 0.197 1.306 3.40e-02 8.65e+02 1.48e+03 bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.628 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.306 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" N PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 1.473 1.588 -0.115 1.40e-02 5.10e+03 6.76e+01 bond pdb=" N PRO A 829 " pdb=" CA PRO A 829 " ideal model delta sigma weight residual 1.471 1.371 0.100 1.32e-02 5.74e+03 5.70e+01 ... (remaining 10250 not shown) Histogram of bond angle deviations from ideal: 59.41 - 74.53: 1 74.53 - 89.65: 2 89.65 - 104.77: 186 104.77 - 119.89: 8932 119.89 - 135.01: 4788 Bond angle restraints: 13909 Sorted by residual: angle pdb=" N PRO A 829 " pdb=" CD PRO A 829 " pdb=" CG PRO A 829 " ideal model delta sigma weight residual 103.20 59.41 43.79 1.50e+00 4.44e-01 8.52e+02 angle pdb=" CA PRO A 829 " pdb=" N PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 112.00 92.69 19.31 1.40e+00 5.10e-01 1.90e+02 angle pdb=" CA PRO A 829 " pdb=" CB PRO A 829 " pdb=" CG PRO A 829 " ideal model delta sigma weight residual 104.50 79.23 25.27 1.90e+00 2.77e-01 1.77e+02 angle pdb=" N PRO A 829 " pdb=" CA PRO A 829 " pdb=" CB PRO A 829 " ideal model delta sigma weight residual 103.48 94.95 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" CB PRO A 829 " pdb=" CG PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 106.10 81.78 24.32 3.20e+00 9.77e-02 5.78e+01 ... (remaining 13904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 5410 19.44 - 38.87: 618 38.87 - 58.31: 116 58.31 - 77.75: 30 77.75 - 97.18: 11 Dihedral angle restraints: 6185 sinusoidal: 2497 harmonic: 3688 Sorted by residual: dihedral pdb=" CA SER A 444 " pdb=" C SER A 444 " pdb=" N ALA A 445 " pdb=" CA ALA A 445 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 442 " pdb=" C SER A 442 " pdb=" N GLU A 443 " pdb=" CA GLU A 443 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLN G 35 " pdb=" C GLN G 35 " pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1437 0.072 - 0.144: 135 0.144 - 0.215: 1 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA PRO A 829 " pdb=" N PRO A 829 " pdb=" C PRO A 829 " pdb=" CB PRO A 829 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1572 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 828 " 0.089 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 829 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 174 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C GLU A 174 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 174 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 175 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 444 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C SER A 444 " 0.047 2.00e-02 2.50e+03 pdb=" O SER A 444 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 445 " -0.016 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 550 2.73 - 3.27: 10096 3.27 - 3.81: 16167 3.81 - 4.36: 18953 4.36 - 4.90: 33588 Nonbonded interactions: 79354 Sorted by model distance: nonbonded pdb=" OG1 THR A 804 " pdb=" OE1 GLN A 920 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.211 2.440 nonbonded pdb=" O VAL A 129 " pdb=" OG1 THR A 133 " model vdw 2.216 2.440 nonbonded pdb=" O LEU A 86 " pdb=" OG SER A 91 " model vdw 2.233 2.440 nonbonded pdb=" N GLU B 197 " pdb=" OE1 GLU B 197 " model vdw 2.243 2.520 ... (remaining 79349 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 group one per residue 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: 0.760 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: 2.970 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.770 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.014 1.306 10255 Z= 1.050 Angle : 0.840 43.794 13909 Z= 0.453 Chirality : 0.043 0.359 1575 Planarity : 0.005 0.120 1787 Dihedral : 17.167 97.183 3811 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 25.23 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.26 (0.24), residues: 1273 helix: 1.03 (0.24), residues: 528 sheet: -1.16 (0.41), residues: 144 loop : -0.97 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.012 0.001 TYR A 478 ARG 0.004 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.306 Fit side-chains REVERT: A 434 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8782 (ttpp) REVERT: A 923 ASP cc_start: 0.8605 (t0) cc_final: 0.8220 (t0) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2333 time to fit residues: 41.0909 Evaluate side-chains 122 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 413 HIS A 427 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN A 687 GLN A 872 ASN A 886 ASN B 104 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10255 Z= 0.332 Angle : 0.596 9.562 13909 Z= 0.312 Chirality : 0.044 0.144 1575 Planarity : 0.005 0.063 1787 Dihedral : 7.870 98.642 1412 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.02 % Allowed : 22.39 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.41 (0.24), residues: 1273 helix: 0.90 (0.24), residues: 524 sheet: -1.20 (0.42), residues: 144 loop : -1.06 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.004 0.001 HIS A 483 PHE 0.013 0.002 PHE A 297 TYR 0.015 0.001 TYR A 859 ARG 0.003 0.000 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.185 Fit side-chains REVERT: A 132 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 434 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8786 (ttpp) REVERT: A 466 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6544 (pttt) REVERT: A 469 GLU cc_start: 0.7147 (tp30) cc_final: 0.6893 (mp0) REVERT: B 110 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: B 177 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8852 (mp) outliers start: 44 outliers final: 25 residues processed: 161 average time/residue: 0.2162 time to fit residues: 49.4192 Evaluate side-chains 145 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 199 HIS A 223 HIS A 396 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10255 Z= 0.185 Angle : 0.522 7.189 13909 Z= 0.271 Chirality : 0.041 0.142 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.448 94.351 1412 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.74 % Allowed : 23.67 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.24 (0.24), residues: 1273 helix: 1.00 (0.24), residues: 523 sheet: -1.02 (0.41), residues: 142 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 307 HIS 0.004 0.001 HIS A 483 PHE 0.013 0.001 PHE A 297 TYR 0.013 0.001 TYR A 478 ARG 0.003 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.168 Fit side-chains REVERT: A 132 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8483 (mt) REVERT: A 434 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8828 (ttpp) REVERT: A 469 GLU cc_start: 0.7165 (tp30) cc_final: 0.6707 (mp0) REVERT: A 549 TYR cc_start: 0.7674 (m-80) cc_final: 0.7349 (m-80) REVERT: A 923 ASP cc_start: 0.8516 (t0) cc_final: 0.7946 (t0) REVERT: B 110 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: B 177 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8836 (mp) outliers start: 30 outliers final: 17 residues processed: 154 average time/residue: 0.2162 time to fit residues: 47.7295 Evaluate side-chains 142 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 199 HIS A 479 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10255 Z= 0.184 Angle : 0.512 7.210 13909 Z= 0.265 Chirality : 0.041 0.212 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.248 92.747 1412 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.47 % Allowed : 23.58 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.17 (0.24), residues: 1273 helix: 1.08 (0.24), residues: 523 sheet: -1.10 (0.41), residues: 147 loop : -0.89 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.014 0.001 PHE A 297 TYR 0.018 0.001 TYR A 478 ARG 0.002 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.292 Fit side-chains REVERT: A 132 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 434 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8838 (ttpp) REVERT: A 480 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6643 (mm) REVERT: A 549 TYR cc_start: 0.7667 (m-80) cc_final: 0.7393 (m-80) REVERT: B 110 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: B 177 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8823 (mp) outliers start: 38 outliers final: 25 residues processed: 154 average time/residue: 0.2049 time to fit residues: 45.9578 Evaluate side-chains 147 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.1980 chunk 69 optimal weight: 0.0060 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 199 HIS A 491 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10255 Z= 0.153 Angle : 0.499 7.073 13909 Z= 0.258 Chirality : 0.041 0.196 1575 Planarity : 0.004 0.043 1787 Dihedral : 7.148 92.710 1412 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.93 % Allowed : 24.59 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.08 (0.24), residues: 1273 helix: 1.17 (0.24), residues: 524 sheet: -1.04 (0.40), residues: 147 loop : -0.85 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.007 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.015 0.001 TYR A 478 ARG 0.002 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.213 Fit side-chains REVERT: A 132 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8416 (mt) REVERT: A 434 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8868 (ttpp) REVERT: B 110 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6815 (tp30) REVERT: B 177 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8782 (mp) outliers start: 32 outliers final: 20 residues processed: 155 average time/residue: 0.2185 time to fit residues: 48.2539 Evaluate side-chains 141 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10255 Z= 0.226 Angle : 0.530 7.361 13909 Z= 0.273 Chirality : 0.042 0.193 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.220 94.752 1412 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.29 % Allowed : 24.41 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.15 (0.24), residues: 1273 helix: 1.08 (0.24), residues: 523 sheet: -1.01 (0.41), residues: 147 loop : -0.88 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.014 0.001 TYR A 859 ARG 0.004 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.209 Fit side-chains REVERT: A 132 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 434 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8864 (ttpp) REVERT: A 637 ARG cc_start: 0.6863 (tmm-80) cc_final: 0.6602 (ttt-90) REVERT: A 677 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: B 110 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: B 177 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8791 (mp) outliers start: 36 outliers final: 27 residues processed: 154 average time/residue: 0.2024 time to fit residues: 45.3802 Evaluate side-chains 149 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10255 Z= 0.249 Angle : 0.552 8.891 13909 Z= 0.283 Chirality : 0.042 0.192 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.313 96.607 1412 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.38 % Allowed : 24.95 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.21 (0.24), residues: 1273 helix: 1.03 (0.24), residues: 523 sheet: -1.04 (0.41), residues: 147 loop : -0.92 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 307 HIS 0.010 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.018 0.001 TYR A 478 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.107 Fit side-chains REVERT: A 132 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 412 SER cc_start: 0.8100 (p) cc_final: 0.7864 (t) REVERT: A 434 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8904 (ttpp) REVERT: A 518 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 529 GLN cc_start: 0.8483 (tp40) cc_final: 0.8276 (tp40) REVERT: A 637 ARG cc_start: 0.6849 (tmm-80) cc_final: 0.6573 (ttt-90) REVERT: B 110 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6766 (tp30) REVERT: B 177 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8785 (mp) outliers start: 37 outliers final: 27 residues processed: 151 average time/residue: 0.2032 time to fit residues: 44.5822 Evaluate side-chains 148 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 96 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10255 Z= 0.163 Angle : 0.515 7.146 13909 Z= 0.267 Chirality : 0.041 0.169 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.150 95.891 1412 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.56 % Allowed : 26.05 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.08 (0.24), residues: 1273 helix: 1.16 (0.24), residues: 524 sheet: -0.97 (0.41), residues: 147 loop : -0.87 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.014 0.001 PHE A 297 TYR 0.012 0.001 TYR A 859 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.116 Fit side-chains REVERT: A 132 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 412 SER cc_start: 0.8126 (p) cc_final: 0.7802 (t) REVERT: A 434 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8888 (ttpp) REVERT: A 518 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: A 637 ARG cc_start: 0.6854 (tmm-80) cc_final: 0.6550 (ttt-90) REVERT: B 177 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8769 (mp) outliers start: 28 outliers final: 22 residues processed: 146 average time/residue: 0.2085 time to fit residues: 44.2452 Evaluate side-chains 142 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 114 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10255 Z= 0.163 Angle : 0.521 7.819 13909 Z= 0.268 Chirality : 0.041 0.164 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.100 95.670 1412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.65 % Allowed : 26.23 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.02 (0.24), residues: 1273 helix: 1.21 (0.24), residues: 524 sheet: -0.97 (0.40), residues: 147 loop : -0.84 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.020 0.001 TYR A 478 ARG 0.003 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.237 Fit side-chains REVERT: A 132 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8316 (mt) REVERT: A 412 SER cc_start: 0.8133 (p) cc_final: 0.7802 (t) REVERT: A 434 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8883 (ttpp) REVERT: A 518 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 637 ARG cc_start: 0.6792 (tmm-80) cc_final: 0.6433 (ttt-90) REVERT: B 177 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8767 (mp) outliers start: 29 outliers final: 23 residues processed: 140 average time/residue: 0.2250 time to fit residues: 46.1747 Evaluate side-chains 142 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10255 Z= 0.160 Angle : 0.515 7.677 13909 Z= 0.265 Chirality : 0.041 0.158 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.050 95.587 1412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.65 % Allowed : 25.96 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.05 (0.24), residues: 1273 helix: 1.30 (0.24), residues: 518 sheet: -0.94 (0.40), residues: 147 loop : -0.80 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.014 0.001 PHE A 297 TYR 0.013 0.001 TYR A 859 ARG 0.004 0.000 ARG B 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.213 Fit side-chains REVERT: A 132 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 412 SER cc_start: 0.8135 (p) cc_final: 0.7859 (t) REVERT: A 434 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8884 (ttpp) REVERT: A 518 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: A 637 ARG cc_start: 0.6791 (tmm-80) cc_final: 0.6353 (ttt-90) REVERT: B 177 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8764 (mp) outliers start: 29 outliers final: 23 residues processed: 145 average time/residue: 0.2657 time to fit residues: 56.7814 Evaluate side-chains 140 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126240 restraints weight = 21981.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124325 restraints weight = 31229.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121470 restraints weight = 17129.086| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10255 Z= 0.181 Angle : 0.533 7.552 13909 Z= 0.273 Chirality : 0.041 0.152 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.035 95.763 1412 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.74 % Allowed : 26.05 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.03 (0.24), residues: 1273 helix: 1.27 (0.24), residues: 518 sheet: -0.92 (0.41), residues: 147 loop : -0.80 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.013 0.001 TYR A 859 ARG 0.004 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.99 seconds wall clock time: 40 minutes 51.37 seconds (2451.37 seconds total)