Starting phenix.real_space_refine on Fri Feb 16 16:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7at8_11910/02_2024/7at8_11910_updated.pdb" } resolution = 4.4 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= 0.002 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 7 6.06 5 P 310 5.49 5 S 55 5.16 5 C 9053 2.51 5 N 2945 2.21 5 O 3581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C ASP 605": "OD1" <-> "OD2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15951 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain breaks: 6 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 13, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1024 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "F" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "I" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3176 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "U" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 33 Unusual residues: {' ZN': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 222 SG CYS A 286 42.792 44.930 98.704 1.00172.70 S ATOM 250 SG CYS A 289 39.019 44.911 98.087 0.99172.87 S ATOM 296 SG CYS A 294 41.047 41.721 97.546 0.87165.55 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 958 SG CYS A 567 55.456 57.195 95.986 1.00196.50 S ATOM 985 SG CYS A 571 57.977 58.482 93.473 1.00189.83 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 841 SG CYS A 552 60.285 52.403 95.140 1.00211.70 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 854 SG CYS A 554 56.701 51.050 93.445 0.93198.28 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 943 SG CYS A 565 53.618 52.936 94.782 1.00180.30 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1255 SG CYS A 606 40.534 60.860 80.840 1.00151.54 S ATOM 1351 SG CYS A 619 39.256 57.835 79.458 1.00148.68 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1139 SG CYS A 591 46.636 58.342 81.480 1.00155.72 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1234 SG CYS A 603 44.045 59.728 83.596 1.00143.87 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1058 SG CYS A 580 44.717 62.660 76.821 1.00142.11 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1126 SG CYS A 589 45.819 59.144 77.101 1.00147.49 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA D 31 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA D 31 " occ=0.00 residue: pdb=" N THR D 32 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR D 32 " occ=0.00 Time building chain proxies: 8.55, per 1000 atoms: 0.54 Number of scatterers: 15951 At special positions: 0 Unit cell: (130.95, 171.108, 144.918, 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 7 29.99 S 55 16.00 P 310 15.00 O 3581 8.00 N 2945 7.00 C 9053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 289 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 286 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 294 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 567 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 571 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 561 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 543 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 552 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 565 " pdb=" ZN A1005 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 619 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 606 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 584 " pdb=" ZN A1006 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 603 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 591 " pdb=" ZN A1007 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 589 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 580 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 584 " Number of angles added : 36 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 3 sheets defined 53.5% alpha, 2.8% beta 150 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.521A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.736A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 removed outlier: 3.673A pdb=" N ARG A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 553 through 556 No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 623 through 626 No H-bonds generated for 'chain 'A' and resid 623 through 626' Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.545A pdb=" N ASP A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'C' and resid 590 through 601 removed outlier: 3.640A pdb=" N GLU C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 624 removed outlier: 5.156A pdb=" N VAL C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 614 " --> pdb=" O LYS C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 649 removed outlier: 3.838A pdb=" N ASN C 633 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 639 " --> pdb=" O CYS C 636 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C 642 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR C 643 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLY C 644 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN C 645 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 665 Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.920A pdb=" N ASP C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 64 through 78 removed outlier: 3.699A pdb=" N ASP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'E' and resid 25 through 28 Processing helix chain 'E' and resid 31 through 41 Processing helix chain 'E' and resid 50 through 75 Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'F' and resid 18 through 21 No H-bonds generated for 'chain 'F' and resid 18 through 21' Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 46 through 72 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'G' and resid 35 through 45 Processing helix chain 'G' and resid 53 through 80 Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 101 through 120 Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 64 through 78 removed outlier: 3.793A pdb=" N ASP H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 41 Processing helix chain 'I' and resid 50 through 75 Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'J' and resid 17 through 21 Processing helix chain 'J' and resid 27 through 36 Processing helix chain 'J' and resid 47 through 73 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 92 through 96 Processing helix chain 'K' and resid 35 through 45 Processing helix chain 'K' and resid 53 through 80 Processing helix chain 'K' and resid 88 through 98 Processing helix chain 'K' and resid 101 through 120 Processing sheet with id= A, first strand: chain 'A' and resid 632 through 636 Processing sheet with id= B, first strand: chain 'A' and resid 662 through 665 Processing sheet with id= C, first strand: chain 'A' and resid 713 through 720 removed outlier: 6.216A pdb=" N ALA A 730 " --> pdb=" O PHE A 655 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 655 " --> pdb=" O ALA A 730 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 766 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 9.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3729 1.33 - 1.45: 4551 1.45 - 1.57: 7896 1.57 - 1.69: 620 1.69 - 1.81: 80 Bond restraints: 16876 Sorted by residual: bond pdb=" N ASN C 607 " pdb=" CA ASN C 607 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N VAL C 581 " pdb=" CA VAL C 581 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" C2 SAH A1008 " pdb=" N3 SAH A1008 " ideal model delta sigma weight residual 1.322 1.383 -0.061 2.00e-02 2.50e+03 9.24e+00 bond pdb=" N VAL A 755 " pdb=" CA VAL A 755 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.16e+00 bond pdb=" N LYS A 753 " pdb=" CA LYS A 753 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.81e+00 ... (remaining 16871 not shown) Histogram of bond angle deviations from ideal: 91.73 - 100.18: 21 100.18 - 108.62: 3518 108.62 - 117.07: 9848 117.07 - 125.52: 9632 125.52 - 133.96: 1100 Bond angle restraints: 24119 Sorted by residual: angle pdb=" N ASP C 585 " pdb=" CA ASP C 585 " pdb=" C ASP C 585 " ideal model delta sigma weight residual 109.56 102.09 7.47 1.84e+00 2.95e-01 1.65e+01 angle pdb=" O3' DA U -66 " pdb=" P DT U -65 " pdb=" O5' DT U -65 " ideal model delta sigma weight residual 104.00 97.94 6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C ASN C 607 " pdb=" N GLU C 608 " pdb=" CA GLU C 608 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" CA LEU A 752 " pdb=" C LEU A 752 " pdb=" O LEU A 752 " ideal model delta sigma weight residual 122.63 118.03 4.60 1.29e+00 6.01e-01 1.27e+01 angle pdb=" C GLU C 580 " pdb=" N VAL C 581 " pdb=" CA VAL C 581 " ideal model delta sigma weight residual 121.97 128.19 -6.22 1.80e+00 3.09e-01 1.19e+01 ... (remaining 24114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 6869 18.23 - 36.46: 1167 36.46 - 54.69: 1069 54.69 - 72.91: 240 72.91 - 91.14: 12 Dihedral angle restraints: 9357 sinusoidal: 5864 harmonic: 3493 Sorted by residual: dihedral pdb=" CA PHE C 603 " pdb=" C PHE C 603 " pdb=" N SER C 604 " pdb=" CA SER C 604 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN C 562 " pdb=" C ASN C 562 " pdb=" N ARG C 563 " pdb=" CA ARG C 563 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE C 627 " pdb=" C ILE C 627 " pdb=" N ALA C 628 " pdb=" CA ALA C 628 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 9354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2192 0.047 - 0.095: 447 0.095 - 0.142: 58 0.142 - 0.189: 7 0.189 - 0.237: 2 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA VAL C 606 " pdb=" N VAL C 606 " pdb=" C VAL C 606 " pdb=" CB VAL C 606 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 745 " pdb=" N ARG A 745 " pdb=" C ARG A 745 " pdb=" CB ARG A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" C3' SAH A1008 " pdb=" C2' SAH A1008 " pdb=" C4' SAH A1008 " pdb=" O3' SAH A1008 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2703 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U -27 " -0.032 2.00e-02 2.50e+03 2.96e-02 1.97e+01 pdb=" N1 DC U -27 " 0.072 2.00e-02 2.50e+03 pdb=" C2 DC U -27 " -0.038 2.00e-02 2.50e+03 pdb=" O2 DC U -27 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC U -27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC U -27 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC U -27 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC U -27 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC U -27 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC U 41 " 0.028 2.00e-02 2.50e+03 2.82e-02 1.79e+01 pdb=" N1 DC U 41 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DC U 41 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC U 41 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC U 41 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC U 41 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC U 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT U 14 " 0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT U 14 " -0.070 2.00e-02 2.50e+03 pdb=" C2 DT U 14 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT U 14 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT U 14 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT U 14 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT U 14 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT U 14 " 0.001 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 27 2.39 - 3.02: 8427 3.02 - 3.65: 26489 3.65 - 4.27: 38565 4.27 - 4.90: 57843 Nonbonded interactions: 131351 Sorted by model distance: nonbonded pdb=" O LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 1.763 2.520 nonbonded pdb=" OG1 THR G 29 " pdb=" OP1 DT T 30 " model vdw 2.036 2.440 nonbonded pdb=" C LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 2.068 3.350 nonbonded pdb=" OD1 ASP C 675 " pdb=" N LYS C 676 " model vdw 2.123 2.520 nonbonded pdb=" OE2 GLU A 658 " pdb=" NE ARG A 725 " model vdw 2.209 2.520 ... (remaining 131346 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 'E' and resid 25 through 102) selection = chain 'I' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 16 through 118) } ncs_group { reference = (chain 'G' and resid 29 through 121) selection = chain 'K' } 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=0.00 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: 6.780 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: 0.000 Extract box with map and model: 6.740 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 54.080 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.004 0.061 16876 Z= 0.221 Angle : 0.649 10.036 24119 Z= 0.410 Chirality : 0.038 0.237 2706 Planarity : 0.004 0.030 1989 Dihedral : 24.584 91.143 7093 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.25 % Favored : 97.40 % Rotamer: Outliers : 0.40 % Allowed : 1.29 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1155 helix: 0.52 (0.19), residues: 677 sheet: -3.01 (0.84), residues: 24 loop : -2.40 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 617 HIS 0.008 0.001 HIS I 75 PHE 0.006 0.001 PHE C 603 TYR 0.011 0.001 TYR K 37 ARG 0.014 0.000 ARG C 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 THR cc_start: 0.6129 (m) cc_final: 0.5895 (p) REVERT: A 719 MET cc_start: 0.7885 (tpp) cc_final: 0.7676 (tpp) REVERT: C 632 MET cc_start: 0.8165 (mmp) cc_final: 0.7864 (mmp) REVERT: C 649 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8393 (mttp) REVERT: D 45 THR cc_start: 0.7940 (m) cc_final: 0.7590 (m) REVERT: D 50 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8686 (pt0) REVERT: D 86 SER cc_start: 0.8498 (p) cc_final: 0.7970 (m) REVERT: D 93 GLN cc_start: 0.9194 (tt0) cc_final: 0.8783 (tt0) REVERT: D 97 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8843 (mt-10) REVERT: D 99 TYR cc_start: 0.8382 (t80) cc_final: 0.7227 (t80) REVERT: D 103 LEU cc_start: 0.9100 (tp) cc_final: 0.8846 (tt) REVERT: D 107 THR cc_start: 0.9501 (m) cc_final: 0.9080 (m) REVERT: D 125 GLN cc_start: 0.9183 (mt0) cc_final: 0.8555 (mm110) REVERT: E 74 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8407 (tp30) REVERT: E 79 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8201 (mmtm) REVERT: F 61 GLU cc_start: 0.8943 (tp30) cc_final: 0.8495 (tp30) REVERT: F 85 LEU cc_start: 0.9349 (mt) cc_final: 0.9144 (mt) REVERT: F 90 ASP cc_start: 0.8123 (t0) cc_final: 0.7450 (t70) REVERT: F 95 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9063 (tmtt) REVERT: F 97 LEU cc_start: 0.9398 (mt) cc_final: 0.9057 (mp) REVERT: G 37 TYR cc_start: 0.8042 (m-80) cc_final: 0.7097 (m-80) REVERT: G 40 LYS cc_start: 0.9065 (mttt) cc_final: 0.8825 (mmtp) REVERT: G 64 ASN cc_start: 0.8973 (m-40) cc_final: 0.8572 (t0) REVERT: G 91 ILE cc_start: 0.9486 (mm) cc_final: 0.9157 (tt) REVERT: G 102 GLU cc_start: 0.7163 (tp30) cc_final: 0.6736 (tp30) REVERT: H 41 TYR cc_start: 0.7768 (m-80) cc_final: 0.7410 (m-80) REVERT: H 80 THR cc_start: 0.7915 (t) cc_final: 0.7683 (t) REVERT: H 120 MET cc_start: 0.7660 (mtt) cc_final: 0.7077 (mtt) REVERT: I 49 LEU cc_start: 0.9027 (mt) cc_final: 0.8382 (mm) REVERT: I 55 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8603 (mtm180) REVERT: I 68 ASP cc_start: 0.8527 (m-30) cc_final: 0.8279 (m-30) REVERT: J 39 TYR cc_start: 0.8113 (m-80) cc_final: 0.7904 (m-80) REVERT: J 56 GLU cc_start: 0.8600 (tt0) cc_final: 0.8384 (tt0) REVERT: J 68 ASN cc_start: 0.7348 (m-40) cc_final: 0.6987 (m-40) REVERT: J 89 ASN cc_start: 0.8737 (m-40) cc_final: 0.8396 (t0) REVERT: J 92 GLU cc_start: 0.7144 (mt-10) cc_final: 0.5820 (mt-10) REVERT: J 94 ASN cc_start: 0.8746 (t0) cc_final: 0.7876 (m-40) REVERT: J 95 LYS cc_start: 0.8987 (tttt) cc_final: 0.8644 (ttpt) REVERT: K 92 GLN cc_start: 0.8800 (tt0) cc_final: 0.8510 (tm-30) outliers start: 4 outliers final: 1 residues processed: 453 average time/residue: 0.3708 time to fit residues: 230.5917 Evaluate side-chains 240 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 74 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN D 68 GLN E 93 GLN F 73 ASN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16876 Z= 0.220 Angle : 0.578 8.649 24119 Z= 0.337 Chirality : 0.035 0.171 2706 Planarity : 0.004 0.054 1989 Dihedral : 28.885 91.581 4740 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 0.20 % Allowed : 3.36 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.24), residues: 1155 helix: 1.21 (0.20), residues: 674 sheet: -2.48 (1.36), residues: 12 loop : -1.71 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 591 HIS 0.009 0.001 HIS A 297 PHE 0.010 0.001 PHE A 456 TYR 0.023 0.001 TYR F 39 ARG 0.008 0.001 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 THR cc_start: 0.7445 (m) cc_final: 0.7216 (p) REVERT: A 719 MET cc_start: 0.7728 (tpp) cc_final: 0.7504 (tpp) REVERT: C 598 THR cc_start: 0.7819 (t) cc_final: 0.7579 (p) REVERT: C 603 PHE cc_start: 0.5901 (m-80) cc_final: 0.5117 (m-80) REVERT: C 672 MET cc_start: 0.8292 (ppp) cc_final: 0.7467 (ppp) REVERT: C 673 SER cc_start: 0.9096 (m) cc_final: 0.8559 (m) REVERT: D 54 TYR cc_start: 0.8502 (m-10) cc_final: 0.8294 (m-10) REVERT: D 60 LEU cc_start: 0.8485 (mt) cc_final: 0.7950 (mt) REVERT: D 68 GLN cc_start: 0.8759 (tt0) cc_final: 0.8440 (pp30) REVERT: D 86 SER cc_start: 0.8979 (p) cc_final: 0.8774 (p) REVERT: D 93 GLN cc_start: 0.9534 (tt0) cc_final: 0.9017 (tt0) REVERT: D 94 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 125 GLN cc_start: 0.8894 (mt0) cc_final: 0.8673 (mm110) REVERT: E 43 VAL cc_start: 0.8947 (t) cc_final: 0.8396 (p) REVERT: E 74 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8381 (tp30) REVERT: E 88 TYR cc_start: 0.8637 (m-10) cc_final: 0.8290 (m-10) REVERT: F 29 ARG cc_start: 0.7280 (mtp85) cc_final: 0.6938 (ttm-80) REVERT: F 61 GLU cc_start: 0.9115 (tp30) cc_final: 0.8625 (tp30) REVERT: F 90 ASP cc_start: 0.8150 (t0) cc_final: 0.7662 (t70) REVERT: G 37 TYR cc_start: 0.7860 (m-80) cc_final: 0.7518 (m-80) REVERT: G 40 LYS cc_start: 0.9026 (mttt) cc_final: 0.8777 (mmtp) REVERT: G 64 ASN cc_start: 0.8966 (m-40) cc_final: 0.8612 (t0) REVERT: G 102 GLU cc_start: 0.7940 (tp30) cc_final: 0.7576 (tp30) REVERT: H 59 GLU cc_start: 0.7437 (pm20) cc_final: 0.7163 (pm20) REVERT: H 105 GLU cc_start: 0.8593 (tp30) cc_final: 0.8072 (tp30) REVERT: H 120 MET cc_start: 0.8071 (mtt) cc_final: 0.7721 (mtt) REVERT: I 43 VAL cc_start: 0.9456 (t) cc_final: 0.9094 (p) REVERT: I 53 GLU cc_start: 0.9074 (pp20) cc_final: 0.8845 (pp20) REVERT: J 56 GLU cc_start: 0.8624 (tt0) cc_final: 0.8350 (tt0) REVERT: J 64 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7815 (tp30) REVERT: J 68 ASN cc_start: 0.7826 (m-40) cc_final: 0.7269 (m-40) REVERT: J 94 ASN cc_start: 0.8869 (t0) cc_final: 0.7879 (m-40) REVERT: J 95 LYS cc_start: 0.9125 (tttt) cc_final: 0.8759 (ttpt) REVERT: J 112 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8797 (mp10) REVERT: K 70 ILE cc_start: 0.9459 (mm) cc_final: 0.9168 (mm) REVERT: K 90 GLU cc_start: 0.9526 (mp0) cc_final: 0.8970 (mp0) REVERT: K 92 GLN cc_start: 0.9073 (tt0) cc_final: 0.8332 (tm-30) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.2957 time to fit residues: 125.1099 Evaluate side-chains 212 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16876 Z= 0.238 Angle : 0.580 8.712 24119 Z= 0.339 Chirality : 0.035 0.171 2706 Planarity : 0.004 0.048 1989 Dihedral : 29.148 94.056 4740 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.25), residues: 1155 helix: 1.32 (0.20), residues: 673 sheet: -2.04 (1.54), residues: 12 loop : -1.43 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 617 HIS 0.008 0.001 HIS A 297 PHE 0.012 0.001 PHE A 474 TYR 0.014 0.001 TYR J 39 ARG 0.018 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 ASN cc_start: 0.9166 (t0) cc_final: 0.8894 (t0) REVERT: A 687 LEU cc_start: 0.9119 (tp) cc_final: 0.8751 (tp) REVERT: A 696 THR cc_start: 0.7859 (m) cc_final: 0.7653 (p) REVERT: A 719 MET cc_start: 0.7960 (tpp) cc_final: 0.7590 (tpp) REVERT: C 603 PHE cc_start: 0.6362 (m-80) cc_final: 0.5507 (m-80) REVERT: C 657 MET cc_start: 0.5024 (mmp) cc_final: 0.4816 (mmp) REVERT: D 86 SER cc_start: 0.9009 (p) cc_final: 0.8749 (p) REVERT: D 90 MET cc_start: 0.8532 (mmp) cc_final: 0.7895 (mmp) REVERT: D 93 GLN cc_start: 0.9164 (tt0) cc_final: 0.7746 (tt0) REVERT: D 97 GLU cc_start: 0.8829 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 99 TYR cc_start: 0.8637 (t80) cc_final: 0.7698 (t80) REVERT: D 120 MET cc_start: 0.8515 (mmm) cc_final: 0.7968 (mmm) REVERT: E 63 GLU cc_start: 0.8774 (tp30) cc_final: 0.8558 (tp30) REVERT: E 74 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8582 (tp30) REVERT: E 88 TYR cc_start: 0.8335 (m-10) cc_final: 0.7660 (m-10) REVERT: E 95 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6252 (mmt180) REVERT: F 29 ARG cc_start: 0.6543 (mtp85) cc_final: 0.5825 (ttm-80) REVERT: F 38 ASN cc_start: 0.8675 (m110) cc_final: 0.8451 (m110) REVERT: F 61 GLU cc_start: 0.9033 (tp30) cc_final: 0.8566 (tp30) REVERT: F 94 ASN cc_start: 0.8957 (m-40) cc_final: 0.8576 (m-40) REVERT: F 97 LEU cc_start: 0.9173 (mp) cc_final: 0.8928 (mp) REVERT: G 40 LYS cc_start: 0.9277 (mttt) cc_final: 0.8973 (mmtp) REVERT: G 64 ASN cc_start: 0.9084 (m-40) cc_final: 0.8720 (t0) REVERT: H 76 GLN cc_start: 0.7772 (mt0) cc_final: 0.7500 (mt0) REVERT: H 105 GLU cc_start: 0.8745 (tp30) cc_final: 0.8100 (tp30) REVERT: I 43 VAL cc_start: 0.9589 (t) cc_final: 0.9367 (p) REVERT: I 65 VAL cc_start: 0.8976 (t) cc_final: 0.8714 (p) REVERT: J 39 TYR cc_start: 0.8991 (m-80) cc_final: 0.8599 (m-80) REVERT: J 56 GLU cc_start: 0.8453 (tt0) cc_final: 0.8177 (tt0) REVERT: J 64 GLU cc_start: 0.8823 (tm-30) cc_final: 0.7924 (tm-30) REVERT: J 68 ASN cc_start: 0.8201 (m-40) cc_final: 0.7782 (m-40) REVERT: J 94 ASN cc_start: 0.8764 (t0) cc_final: 0.7801 (m-40) REVERT: J 95 LYS cc_start: 0.9280 (tttt) cc_final: 0.8879 (ttpt) REVERT: J 112 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8642 (mp10) REVERT: K 44 GLN cc_start: 0.9222 (tm-30) cc_final: 0.9001 (tm-30) REVERT: K 49 THR cc_start: 0.7230 (m) cc_final: 0.6723 (p) REVERT: K 61 SER cc_start: 0.9284 (t) cc_final: 0.9000 (t) REVERT: K 70 ILE cc_start: 0.9573 (mm) cc_final: 0.9344 (mm) REVERT: K 90 GLU cc_start: 0.9477 (mp0) cc_final: 0.8968 (mp0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3045 time to fit residues: 115.0506 Evaluate side-chains 207 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 0.0010 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 85 GLN H 125 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16876 Z= 0.219 Angle : 0.569 8.152 24119 Z= 0.334 Chirality : 0.035 0.202 2706 Planarity : 0.004 0.049 1989 Dihedral : 29.208 94.504 4740 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.25), residues: 1155 helix: 1.33 (0.20), residues: 685 sheet: -0.89 (1.65), residues: 10 loop : -1.14 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 617 HIS 0.007 0.001 HIS C 659 PHE 0.012 0.001 PHE A 290 TYR 0.012 0.001 TYR A 754 ARG 0.007 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 ASN cc_start: 0.9144 (t0) cc_final: 0.8924 (t0) REVERT: A 687 LEU cc_start: 0.9053 (tp) cc_final: 0.8664 (tp) REVERT: A 696 THR cc_start: 0.7830 (m) cc_final: 0.7614 (p) REVERT: A 719 MET cc_start: 0.8018 (tpp) cc_final: 0.7620 (tpp) REVERT: C 637 MET cc_start: 0.8665 (mmt) cc_final: 0.8387 (mpp) REVERT: C 649 LYS cc_start: 0.7847 (mttp) cc_final: 0.7209 (mttp) REVERT: C 663 MET cc_start: 0.4317 (mtt) cc_final: 0.3950 (mtp) REVERT: D 60 LEU cc_start: 0.8480 (mt) cc_final: 0.8054 (mt) REVERT: D 93 GLN cc_start: 0.9164 (tt0) cc_final: 0.8900 (tt0) REVERT: D 99 TYR cc_start: 0.8723 (t80) cc_final: 0.7856 (t80) REVERT: D 107 THR cc_start: 0.9424 (m) cc_final: 0.9181 (m) REVERT: D 122 LYS cc_start: 0.8588 (pttm) cc_final: 0.8278 (pttp) REVERT: D 125 GLN cc_start: 0.8689 (mm110) cc_final: 0.8341 (mp10) REVERT: E 49 LEU cc_start: 0.8826 (mt) cc_final: 0.8119 (mt) REVERT: E 53 GLU cc_start: 0.8364 (mp0) cc_final: 0.7746 (mp0) REVERT: E 63 GLU cc_start: 0.8772 (tp30) cc_final: 0.8519 (tp30) REVERT: E 74 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8498 (tp30) REVERT: E 88 TYR cc_start: 0.8331 (m-10) cc_final: 0.7719 (m-10) REVERT: E 95 ARG cc_start: 0.7125 (mtp85) cc_final: 0.6395 (mmt180) REVERT: F 50 TYR cc_start: 0.8583 (t80) cc_final: 0.8175 (t80) REVERT: F 57 TYR cc_start: 0.9183 (t80) cc_final: 0.8575 (t80) REVERT: F 61 GLU cc_start: 0.9047 (tp30) cc_final: 0.8520 (tp30) REVERT: F 94 ASN cc_start: 0.9023 (m-40) cc_final: 0.8584 (m-40) REVERT: G 37 TYR cc_start: 0.7516 (m-80) cc_final: 0.6979 (m-80) REVERT: G 64 ASN cc_start: 0.9067 (m-40) cc_final: 0.8764 (t0) REVERT: H 76 GLN cc_start: 0.7856 (mt0) cc_final: 0.7594 (mt0) REVERT: H 79 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8582 (mptt) REVERT: H 105 GLU cc_start: 0.8723 (tp30) cc_final: 0.8276 (tp30) REVERT: H 107 THR cc_start: 0.9487 (m) cc_final: 0.9051 (p) REVERT: H 120 MET cc_start: 0.8237 (mtm) cc_final: 0.8034 (mtp) REVERT: J 41 GLU cc_start: 0.8332 (tp30) cc_final: 0.8102 (tp30) REVERT: J 56 GLU cc_start: 0.8420 (tt0) cc_final: 0.8176 (tt0) REVERT: J 64 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8247 (tm-30) REVERT: J 68 ASN cc_start: 0.8343 (m-40) cc_final: 0.7999 (m-40) REVERT: J 87 VAL cc_start: 0.9771 (m) cc_final: 0.9477 (m) REVERT: J 94 ASN cc_start: 0.8693 (t0) cc_final: 0.8305 (m-40) REVERT: J 95 LYS cc_start: 0.9287 (tttt) cc_final: 0.8938 (ttpt) REVERT: J 99 ARG cc_start: 0.7975 (mpt180) cc_final: 0.7536 (mmt180) REVERT: J 112 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8670 (mp10) REVERT: K 49 THR cc_start: 0.7273 (m) cc_final: 0.6705 (p) REVERT: K 90 GLU cc_start: 0.9467 (mp0) cc_final: 0.8924 (mp0) REVERT: K 92 GLN cc_start: 0.9082 (tt0) cc_final: 0.8433 (tm-30) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.3122 time to fit residues: 122.6679 Evaluate side-chains 211 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN H 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16876 Z= 0.304 Angle : 0.644 12.015 24119 Z= 0.371 Chirality : 0.037 0.183 2706 Planarity : 0.005 0.050 1989 Dihedral : 29.505 98.649 4740 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.25), residues: 1155 helix: 1.19 (0.20), residues: 665 sheet: -1.74 (1.56), residues: 12 loop : -1.18 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 617 HIS 0.008 0.001 HIS I 75 PHE 0.011 0.001 PHE H 78 TYR 0.018 0.002 TYR E 98 ARG 0.005 0.001 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7580 (m-10) cc_final: 0.6490 (p90) REVERT: A 537 ASN cc_start: 0.9217 (t0) cc_final: 0.8969 (t0) REVERT: A 687 LEU cc_start: 0.9064 (tp) cc_final: 0.8594 (tp) REVERT: A 719 MET cc_start: 0.7800 (tpp) cc_final: 0.7563 (tpp) REVERT: C 637 MET cc_start: 0.8741 (mmt) cc_final: 0.8503 (mpp) REVERT: C 657 MET cc_start: 0.5031 (mmp) cc_final: 0.4763 (mmt) REVERT: C 663 MET cc_start: 0.5159 (mtt) cc_final: 0.4757 (mtm) REVERT: D 93 GLN cc_start: 0.9070 (tt0) cc_final: 0.7871 (tt0) REVERT: D 97 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8259 (mt-10) REVERT: D 99 TYR cc_start: 0.9020 (t80) cc_final: 0.7979 (t80) REVERT: E 74 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8700 (tp30) REVERT: E 88 TYR cc_start: 0.8496 (m-10) cc_final: 0.7663 (m-10) REVERT: F 57 TYR cc_start: 0.9131 (t80) cc_final: 0.8576 (t80) REVERT: F 61 GLU cc_start: 0.8926 (tp30) cc_final: 0.8606 (tp30) REVERT: G 48 ASP cc_start: 0.8061 (t0) cc_final: 0.7735 (t0) REVERT: G 56 MET cc_start: 0.8956 (tpp) cc_final: 0.8665 (tpp) REVERT: G 64 ASN cc_start: 0.9239 (m-40) cc_final: 0.8835 (t0) REVERT: H 76 GLN cc_start: 0.7677 (mt0) cc_final: 0.7445 (mt0) REVERT: H 105 GLU cc_start: 0.8779 (tp30) cc_final: 0.8164 (tp30) REVERT: H 107 THR cc_start: 0.9500 (m) cc_final: 0.9010 (t) REVERT: J 68 ASN cc_start: 0.8127 (m-40) cc_final: 0.7699 (m110) REVERT: J 94 ASN cc_start: 0.8788 (t0) cc_final: 0.8545 (m110) REVERT: J 95 LYS cc_start: 0.9366 (tttt) cc_final: 0.8691 (tppt) REVERT: J 99 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7457 (mmt180) REVERT: J 112 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8590 (mp10) REVERT: K 49 THR cc_start: 0.7151 (m) cc_final: 0.6800 (p) REVERT: K 90 GLU cc_start: 0.9420 (mp0) cc_final: 0.8917 (mp0) REVERT: K 92 GLN cc_start: 0.9188 (tt0) cc_final: 0.8410 (tm-30) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3086 time to fit residues: 108.7644 Evaluate side-chains 188 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16876 Z= 0.200 Angle : 0.567 7.197 24119 Z= 0.333 Chirality : 0.035 0.169 2706 Planarity : 0.004 0.052 1989 Dihedral : 29.379 98.524 4740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.26), residues: 1155 helix: 1.41 (0.20), residues: 674 sheet: -0.52 (1.63), residues: 10 loop : -1.05 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 617 HIS 0.009 0.001 HIS A 297 PHE 0.011 0.001 PHE A 685 TYR 0.016 0.001 TYR E 98 ARG 0.002 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 ASN cc_start: 0.9193 (t0) cc_final: 0.8814 (t0) REVERT: A 687 LEU cc_start: 0.9080 (tp) cc_final: 0.8707 (tp) REVERT: A 719 MET cc_start: 0.8058 (tpp) cc_final: 0.7657 (tpp) REVERT: C 603 PHE cc_start: 0.6351 (m-80) cc_final: 0.6052 (m-80) REVERT: C 630 ASN cc_start: 0.7614 (p0) cc_final: 0.7192 (p0) REVERT: C 637 MET cc_start: 0.8692 (mmt) cc_final: 0.8460 (mpp) REVERT: C 663 MET cc_start: 0.5733 (mtt) cc_final: 0.5417 (ptm) REVERT: D 93 GLN cc_start: 0.9187 (tt0) cc_final: 0.8079 (tt0) REVERT: D 97 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8397 (mt-10) REVERT: E 49 LEU cc_start: 0.9159 (mt) cc_final: 0.8097 (mt) REVERT: E 53 GLU cc_start: 0.8618 (mp0) cc_final: 0.7957 (mp0) REVERT: E 88 TYR cc_start: 0.8353 (m-10) cc_final: 0.7607 (m-10) REVERT: E 95 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6617 (mmt180) REVERT: F 50 TYR cc_start: 0.8304 (t80) cc_final: 0.7884 (t80) REVERT: F 56 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8760 (mm-30) REVERT: F 57 TYR cc_start: 0.9016 (t80) cc_final: 0.8635 (t80) REVERT: F 61 GLU cc_start: 0.8924 (tp30) cc_final: 0.8610 (tp30) REVERT: F 64 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8831 (mm-30) REVERT: G 64 ASN cc_start: 0.9075 (m-40) cc_final: 0.8669 (t0) REVERT: H 76 GLN cc_start: 0.7880 (mt0) cc_final: 0.7622 (mt0) REVERT: H 107 THR cc_start: 0.9417 (m) cc_final: 0.9011 (p) REVERT: H 115 LYS cc_start: 0.8584 (tmtt) cc_final: 0.7926 (mmmm) REVERT: J 24 GLN cc_start: 0.8960 (mm110) cc_final: 0.8079 (mp10) REVERT: J 39 TYR cc_start: 0.8995 (m-80) cc_final: 0.8770 (m-80) REVERT: J 41 GLU cc_start: 0.8332 (tp30) cc_final: 0.8073 (tp30) REVERT: J 68 ASN cc_start: 0.8146 (m-40) cc_final: 0.7776 (m-40) REVERT: J 92 GLU cc_start: 0.6853 (tt0) cc_final: 0.6379 (tt0) REVERT: J 94 ASN cc_start: 0.8828 (t0) cc_final: 0.8231 (m-40) REVERT: J 95 LYS cc_start: 0.9264 (tttt) cc_final: 0.8596 (tppt) REVERT: J 99 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7361 (mmt180) REVERT: J 100 VAL cc_start: 0.9591 (t) cc_final: 0.9197 (p) REVERT: J 112 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8591 (mp10) REVERT: K 49 THR cc_start: 0.7125 (m) cc_final: 0.6664 (p) REVERT: K 79 HIS cc_start: 0.7485 (m170) cc_final: 0.7213 (m170) REVERT: K 90 GLU cc_start: 0.9503 (mp0) cc_final: 0.9009 (mp0) REVERT: K 92 GLN cc_start: 0.9161 (tt0) cc_final: 0.8395 (tm-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3052 time to fit residues: 110.5778 Evaluate side-chains 198 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 0.0050 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16876 Z= 0.176 Angle : 0.558 6.895 24119 Z= 0.325 Chirality : 0.034 0.172 2706 Planarity : 0.004 0.054 1989 Dihedral : 29.222 99.532 4740 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.26), residues: 1155 helix: 1.44 (0.20), residues: 689 sheet: -0.40 (1.59), residues: 10 loop : -0.87 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 591 HIS 0.007 0.001 HIS I 75 PHE 0.012 0.001 PHE C 656 TYR 0.015 0.001 TYR E 98 ARG 0.003 0.000 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 ASN cc_start: 0.9104 (t0) cc_final: 0.8717 (t0) REVERT: A 680 MET cc_start: 0.8033 (mmm) cc_final: 0.6998 (mtp) REVERT: A 687 LEU cc_start: 0.9066 (tp) cc_final: 0.8733 (tp) REVERT: A 719 MET cc_start: 0.8018 (tpp) cc_final: 0.7634 (tpp) REVERT: C 663 MET cc_start: 0.5797 (mtt) cc_final: 0.5193 (ptm) REVERT: D 93 GLN cc_start: 0.9339 (tt0) cc_final: 0.8450 (tt0) REVERT: D 97 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8346 (mt-10) REVERT: D 99 TYR cc_start: 0.8889 (t80) cc_final: 0.7930 (t80) REVERT: D 107 THR cc_start: 0.9421 (m) cc_final: 0.9132 (m) REVERT: D 122 LYS cc_start: 0.8550 (pttm) cc_final: 0.8148 (pttp) REVERT: D 125 GLN cc_start: 0.8657 (mm110) cc_final: 0.8306 (mp10) REVERT: E 49 LEU cc_start: 0.8849 (mt) cc_final: 0.8451 (mt) REVERT: E 53 GLU cc_start: 0.8358 (mp0) cc_final: 0.7925 (mp0) REVERT: E 68 ASP cc_start: 0.7726 (m-30) cc_final: 0.7503 (m-30) REVERT: E 88 TYR cc_start: 0.8582 (m-10) cc_final: 0.7661 (m-10) REVERT: F 50 TYR cc_start: 0.8269 (t80) cc_final: 0.7996 (t80) REVERT: F 56 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8639 (mm-30) REVERT: F 57 TYR cc_start: 0.8968 (t80) cc_final: 0.8645 (t80) REVERT: F 61 GLU cc_start: 0.8948 (tp30) cc_final: 0.8557 (tp30) REVERT: G 64 ASN cc_start: 0.9080 (m-40) cc_final: 0.8672 (t0) REVERT: H 76 GLN cc_start: 0.7597 (mt0) cc_final: 0.7347 (mt0) REVERT: H 79 LYS cc_start: 0.9222 (tmmt) cc_final: 0.8920 (tmtt) REVERT: H 105 GLU cc_start: 0.8686 (tp30) cc_final: 0.8159 (tp30) REVERT: H 107 THR cc_start: 0.9381 (m) cc_final: 0.8965 (p) REVERT: H 115 LYS cc_start: 0.8531 (tmtt) cc_final: 0.7777 (mmmm) REVERT: H 123 ASP cc_start: 0.8638 (m-30) cc_final: 0.8405 (m-30) REVERT: I 65 VAL cc_start: 0.9274 (t) cc_final: 0.8893 (p) REVERT: J 39 TYR cc_start: 0.8880 (m-80) cc_final: 0.8663 (m-80) REVERT: J 41 GLU cc_start: 0.8293 (tp30) cc_final: 0.7999 (tp30) REVERT: J 68 ASN cc_start: 0.8172 (m-40) cc_final: 0.7723 (m-40) REVERT: J 94 ASN cc_start: 0.8804 (t0) cc_final: 0.7747 (m-40) REVERT: J 95 LYS cc_start: 0.9250 (tttt) cc_final: 0.8515 (tppt) REVERT: J 99 ARG cc_start: 0.7878 (mpt180) cc_final: 0.7360 (mmt180) REVERT: J 112 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8543 (mp10) REVERT: K 49 THR cc_start: 0.7018 (m) cc_final: 0.6531 (p) REVERT: K 90 GLU cc_start: 0.9512 (mp0) cc_final: 0.8981 (mp0) REVERT: K 92 GLN cc_start: 0.9118 (tt0) cc_final: 0.8388 (tm-30) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3103 time to fit residues: 114.2863 Evaluate side-chains 201 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 89 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 110 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16876 Z= 0.178 Angle : 0.554 7.166 24119 Z= 0.323 Chirality : 0.034 0.186 2706 Planarity : 0.004 0.055 1989 Dihedral : 29.207 99.620 4740 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.26), residues: 1155 helix: 1.49 (0.21), residues: 676 sheet: -0.31 (1.63), residues: 10 loop : -0.86 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 591 HIS 0.007 0.001 HIS I 75 PHE 0.014 0.001 PHE J 25 TYR 0.013 0.001 TYR E 98 ARG 0.003 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 ASN cc_start: 0.9082 (t0) cc_final: 0.8689 (t0) REVERT: A 687 LEU cc_start: 0.9015 (tp) cc_final: 0.8643 (tp) REVERT: A 719 MET cc_start: 0.8063 (tpp) cc_final: 0.7738 (tpp) REVERT: C 646 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8261 (tptp) REVERT: C 657 MET cc_start: 0.5477 (mmp) cc_final: 0.5255 (mmt) REVERT: C 663 MET cc_start: 0.6198 (mtt) cc_final: 0.5568 (ptm) REVERT: D 50 GLU cc_start: 0.8852 (tp30) cc_final: 0.8644 (tp30) REVERT: D 90 MET cc_start: 0.8451 (mmp) cc_final: 0.8063 (mmp) REVERT: D 93 GLN cc_start: 0.9233 (tt0) cc_final: 0.8446 (tt0) REVERT: D 97 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8379 (mt-10) REVERT: D 99 TYR cc_start: 0.8882 (t80) cc_final: 0.8136 (t80) REVERT: D 109 LEU cc_start: 0.9334 (tp) cc_final: 0.9120 (tt) REVERT: D 125 GLN cc_start: 0.8642 (mm110) cc_final: 0.8316 (mt0) REVERT: E 88 TYR cc_start: 0.8534 (m-10) cc_final: 0.7654 (m-10) REVERT: E 95 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6454 (mmt180) REVERT: F 50 TYR cc_start: 0.8309 (t80) cc_final: 0.7900 (t80) REVERT: F 56 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8635 (mm-30) REVERT: F 57 TYR cc_start: 0.8995 (t80) cc_final: 0.8693 (t80) REVERT: F 61 GLU cc_start: 0.8739 (tp30) cc_final: 0.8486 (tp30) REVERT: G 64 ASN cc_start: 0.9081 (m-40) cc_final: 0.8682 (t0) REVERT: H 76 GLN cc_start: 0.7534 (mt0) cc_final: 0.7178 (mt0) REVERT: H 79 LYS cc_start: 0.8976 (tmmt) cc_final: 0.8699 (tmtt) REVERT: H 105 GLU cc_start: 0.8655 (tp30) cc_final: 0.8158 (tp30) REVERT: H 107 THR cc_start: 0.9403 (m) cc_final: 0.8995 (p) REVERT: H 115 LYS cc_start: 0.8634 (tmtt) cc_final: 0.7794 (mmmm) REVERT: H 120 MET cc_start: 0.8650 (mtm) cc_final: 0.7937 (mpp) REVERT: H 123 ASP cc_start: 0.8586 (m-30) cc_final: 0.8347 (m-30) REVERT: I 65 VAL cc_start: 0.9039 (t) cc_final: 0.8644 (p) REVERT: J 24 GLN cc_start: 0.9004 (mm110) cc_final: 0.8325 (mp10) REVERT: J 39 TYR cc_start: 0.8961 (m-80) cc_final: 0.8715 (m-80) REVERT: J 41 GLU cc_start: 0.8346 (tp30) cc_final: 0.7967 (tp30) REVERT: J 68 ASN cc_start: 0.8159 (m-40) cc_final: 0.7694 (m-40) REVERT: J 94 ASN cc_start: 0.8747 (t0) cc_final: 0.7666 (m-40) REVERT: J 95 LYS cc_start: 0.9208 (tttt) cc_final: 0.8513 (tppt) REVERT: J 99 ARG cc_start: 0.7839 (mpt180) cc_final: 0.7400 (mmt180) REVERT: J 112 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8673 (mp10) REVERT: K 49 THR cc_start: 0.6970 (m) cc_final: 0.6498 (p) REVERT: K 54 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8810 (mmmm) REVERT: K 90 GLU cc_start: 0.9580 (mp0) cc_final: 0.9060 (mp0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3055 time to fit residues: 111.5615 Evaluate side-chains 200 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN H 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 16876 Z= 0.376 Angle : 0.698 8.769 24119 Z= 0.401 Chirality : 0.040 0.189 2706 Planarity : 0.005 0.048 1989 Dihedral : 29.716 105.426 4740 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.25), residues: 1155 helix: 0.83 (0.20), residues: 665 sheet: -0.73 (1.02), residues: 28 loop : -1.02 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 642 HIS 0.008 0.001 HIS I 75 PHE 0.020 0.002 PHE C 639 TYR 0.037 0.002 TYR G 37 ARG 0.005 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7257 (m-10) cc_final: 0.6333 (p90) REVERT: A 537 ASN cc_start: 0.9185 (t0) cc_final: 0.8803 (t0) REVERT: A 687 LEU cc_start: 0.9033 (tp) cc_final: 0.8596 (tp) REVERT: A 719 MET cc_start: 0.7853 (tpp) cc_final: 0.7650 (tpp) REVERT: C 646 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8271 (tptp) REVERT: C 663 MET cc_start: 0.6448 (mtt) cc_final: 0.6004 (ptm) REVERT: D 60 LEU cc_start: 0.8765 (mt) cc_final: 0.8475 (mt) REVERT: D 90 MET cc_start: 0.8684 (mmp) cc_final: 0.8426 (mmp) REVERT: D 93 GLN cc_start: 0.8797 (tt0) cc_final: 0.7759 (tt0) REVERT: D 97 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8161 (mt-10) REVERT: D 99 TYR cc_start: 0.9085 (t80) cc_final: 0.8164 (t80) REVERT: D 105 GLU cc_start: 0.8141 (pp20) cc_final: 0.7500 (pp20) REVERT: D 106 ASP cc_start: 0.8187 (m-30) cc_final: 0.7946 (m-30) REVERT: E 37 LEU cc_start: 0.9773 (mm) cc_final: 0.9510 (mm) REVERT: E 68 ASP cc_start: 0.8056 (m-30) cc_final: 0.7787 (m-30) REVERT: E 88 TYR cc_start: 0.8555 (m-10) cc_final: 0.7770 (m-10) REVERT: F 56 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8730 (mm-30) REVERT: F 57 TYR cc_start: 0.9161 (t80) cc_final: 0.8655 (t80) REVERT: F 61 GLU cc_start: 0.9011 (tp30) cc_final: 0.8760 (tp30) REVERT: F 90 ASP cc_start: 0.8528 (t0) cc_final: 0.8305 (t70) REVERT: G 56 MET cc_start: 0.8919 (tpp) cc_final: 0.8599 (tpp) REVERT: G 64 ASN cc_start: 0.9318 (m-40) cc_final: 0.8854 (t0) REVERT: H 79 LYS cc_start: 0.9058 (tmmt) cc_final: 0.8810 (tmtt) REVERT: H 105 GLU cc_start: 0.8840 (tp30) cc_final: 0.8230 (tp30) REVERT: H 115 LYS cc_start: 0.8582 (tmtt) cc_final: 0.7929 (mmmm) REVERT: I 65 VAL cc_start: 0.8905 (t) cc_final: 0.8568 (p) REVERT: J 56 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7539 (tm-30) REVERT: J 94 ASN cc_start: 0.9039 (t0) cc_final: 0.8410 (m-40) REVERT: J 95 LYS cc_start: 0.9360 (tttt) cc_final: 0.8701 (tppt) REVERT: J 99 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7510 (mmt180) REVERT: K 44 GLN cc_start: 0.9239 (tm-30) cc_final: 0.9008 (tm-30) REVERT: K 49 THR cc_start: 0.6811 (m) cc_final: 0.6400 (p) REVERT: K 54 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8932 (mmmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3207 time to fit residues: 108.2176 Evaluate side-chains 185 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.0170 chunk 92 optimal weight: 0.6980 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16876 Z= 0.188 Angle : 0.594 7.790 24119 Z= 0.342 Chirality : 0.035 0.166 2706 Planarity : 0.004 0.054 1989 Dihedral : 29.440 106.010 4740 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.25), residues: 1155 helix: 1.15 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 591 HIS 0.008 0.001 HIS I 75 PHE 0.016 0.001 PHE J 25 TYR 0.018 0.001 TYR E 98 ARG 0.006 0.000 ARG C 563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7037 (m-10) cc_final: 0.6308 (p90) REVERT: A 537 ASN cc_start: 0.9114 (t0) cc_final: 0.8726 (t0) REVERT: A 687 LEU cc_start: 0.8990 (tp) cc_final: 0.8689 (tp) REVERT: A 719 MET cc_start: 0.8066 (tpp) cc_final: 0.7800 (tpp) REVERT: C 646 LYS cc_start: 0.8823 (mmpt) cc_final: 0.8231 (tptp) REVERT: C 663 MET cc_start: 0.6486 (mtt) cc_final: 0.6075 (ptm) REVERT: D 50 GLU cc_start: 0.8915 (tp30) cc_final: 0.8715 (tp30) REVERT: D 81 ASP cc_start: 0.7975 (t70) cc_final: 0.7674 (t70) REVERT: D 93 GLN cc_start: 0.9226 (tt0) cc_final: 0.8201 (tm-30) REVERT: D 97 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8110 (mt-10) REVERT: D 105 GLU cc_start: 0.7812 (pp20) cc_final: 0.7604 (pp20) REVERT: E 23 ARG cc_start: 0.4885 (mpp-170) cc_final: 0.4571 (mpt180) REVERT: E 49 LEU cc_start: 0.9202 (mt) cc_final: 0.8101 (mt) REVERT: E 53 GLU cc_start: 0.8616 (mp0) cc_final: 0.7937 (mp0) REVERT: E 63 GLU cc_start: 0.8722 (tp30) cc_final: 0.8441 (tp30) REVERT: E 68 ASP cc_start: 0.7834 (m-30) cc_final: 0.7605 (m-30) REVERT: E 74 GLU cc_start: 0.8724 (tp30) cc_final: 0.8351 (tp30) REVERT: E 88 TYR cc_start: 0.8310 (m-10) cc_final: 0.7776 (m-10) REVERT: F 56 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8647 (mm-30) REVERT: F 61 GLU cc_start: 0.8911 (tp30) cc_final: 0.8499 (tp30) REVERT: G 64 ASN cc_start: 0.9077 (m-40) cc_final: 0.8681 (t0) REVERT: G 117 LYS cc_start: 0.9072 (tptm) cc_final: 0.8759 (tppt) REVERT: H 105 GLU cc_start: 0.8840 (tp30) cc_final: 0.8164 (tp30) REVERT: H 115 LYS cc_start: 0.8515 (tmtt) cc_final: 0.7933 (mmmm) REVERT: I 53 GLU cc_start: 0.9191 (pp20) cc_final: 0.8959 (pp20) REVERT: I 65 VAL cc_start: 0.9002 (t) cc_final: 0.8692 (p) REVERT: J 39 TYR cc_start: 0.9113 (m-80) cc_final: 0.8852 (m-80) REVERT: J 41 GLU cc_start: 0.8346 (tp30) cc_final: 0.8041 (tp30) REVERT: J 62 ILE cc_start: 0.9179 (tt) cc_final: 0.8970 (tt) REVERT: J 94 ASN cc_start: 0.9065 (t0) cc_final: 0.7780 (m-40) REVERT: J 95 LYS cc_start: 0.9221 (tttt) cc_final: 0.8617 (tppt) REVERT: J 99 ARG cc_start: 0.7938 (mpt180) cc_final: 0.7345 (mmt180) REVERT: K 49 THR cc_start: 0.6815 (m) cc_final: 0.6350 (p) REVERT: K 54 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8824 (mmmm) REVERT: K 90 GLU cc_start: 0.9557 (mp0) cc_final: 0.9091 (mp0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3136 time to fit residues: 112.6234 Evaluate side-chains 196 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.063569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049975 restraints weight = 96066.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051210 restraints weight = 54651.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052053 restraints weight = 37598.122| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16876 Z= 0.294 Angle : 0.647 7.601 24119 Z= 0.371 Chirality : 0.038 0.233 2706 Planarity : 0.004 0.050 1989 Dihedral : 29.573 110.842 4740 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1155 helix: 0.94 (0.20), residues: 671 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 617 HIS 0.007 0.001 HIS I 75 PHE 0.022 0.002 PHE J 25 TYR 0.034 0.002 TYR G 37 ARG 0.005 0.001 ARG C 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.92 seconds wall clock time: 60 minutes 14.98 seconds (3614.98 seconds total)