Starting phenix.real_space_refine on Thu Sep 18 12:14:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihd_52865/09_2025/9ihd_52865.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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 Fe 1 7.16 5 P 290 5.49 5 S 41 5.16 5 C 9483 2.51 5 N 3075 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16508 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" 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: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.93, per 1000 atoms: 0.24 Number of scatterers: 16508 At special positions: 0 Unit cell: (119.68, 121.04, 133.96, 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) Fe 1 26.01 S 41 16.00 P 290 15.00 O 3618 8.00 N 3075 7.00 C 9483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Links applied NAG-ASN " NAG N 603 " - " ASN N 189 " " NAG N 604 " - " ASN N 317 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 540.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 60.6% alpha, 3.0% beta 134 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.121A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.547A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.877A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.994A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.506A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.671A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.560A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.560A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.720A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.700A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 180 through 188 Processing helix chain 'N' and resid 219 through 225 removed outlier: 3.951A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 310 removed outlier: 5.312A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Proline residue: N 303 - end of helix Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.601A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 399 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 440 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.672A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 removed outlier: 3.633A pdb=" N THR N 541 " --> pdb=" O ILE N 537 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 576 removed outlier: 4.210A pdb=" N SER N 574 " --> pdb=" O ASN N 571 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.151A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.160A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.725A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.010A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.158A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 27 through 28 removed outlier: 3.692A pdb=" N ARG M 27 " --> pdb=" O ASN N 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'M' and resid 78 through 83 removed outlier: 3.970A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AB5, first strand: chain 'N' and resid 546 through 547 555 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 6760 1.39 - 1.57: 10016 1.57 - 1.75: 578 1.75 - 1.93: 69 1.93 - 2.11: 4 Bond restraints: 17427 Sorted by residual: bond pdb=" CGA HEM N 601 " pdb=" O2A HEM N 601 " ideal model delta sigma weight residual 1.258 1.306 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C3' DC J -21 " pdb=" O3' DC J -21 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" C3' DC J 44 " pdb=" O3' DC J 44 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" C3' DA J -22 " pdb=" O3' DA J -22 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 17422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 24724 2.88 - 5.77: 89 5.77 - 8.65: 8 8.65 - 11.53: 3 11.53 - 14.41: 2 Bond angle restraints: 24826 Sorted by residual: angle pdb=" N ASN N 189 " pdb=" CA ASN N 189 " pdb=" C ASN N 189 " ideal model delta sigma weight residual 110.65 104.72 5.93 1.26e+00 6.30e-01 2.21e+01 angle pdb=" CA ARG N 333 " pdb=" CB ARG N 333 " pdb=" CG ARG N 333 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CB MET N 243 " pdb=" CG MET N 243 " pdb=" SD MET N 243 " ideal model delta sigma weight residual 112.70 104.64 8.06 3.00e+00 1.11e-01 7.21e+00 angle pdb=" CBA HEM N 601 " pdb=" CGA HEM N 601 " pdb=" O2A HEM N 601 " ideal model delta sigma weight residual 118.50 126.30 -7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" CA LEU M 22 " pdb=" CB LEU M 22 " pdb=" CG LEU M 22 " ideal model delta sigma weight residual 116.30 125.11 -8.81 3.50e+00 8.16e-02 6.33e+00 ... (remaining 24821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8241 35.32 - 70.65: 1542 70.65 - 105.97: 17 105.97 - 141.30: 2 141.30 - 176.62: 6 Dihedral angle restraints: 9808 sinusoidal: 5996 harmonic: 3812 Sorted by residual: dihedral pdb=" C4' DC J 44 " pdb=" C3' DC J 44 " pdb=" O3' DC J 44 " pdb=" P DC J 45 " ideal model delta sinusoidal sigma weight residual -140.00 36.62 -176.62 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J -21 " pdb=" C3' DC J -21 " pdb=" O3' DC J -21 " pdb=" P DC J -20 " ideal model delta sinusoidal sigma weight residual 220.00 54.93 165.07 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -31 " pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " pdb=" P DG J -30 " ideal model delta sinusoidal sigma weight residual 220.00 63.87 156.13 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2775 0.125 - 0.249: 7 0.249 - 0.374: 0 0.374 - 0.499: 0 0.499 - 0.623: 1 Chirality restraints: 2783 Sorted by residual: chirality pdb=" C1 NAG N 603 " pdb=" ND2 ASN N 189 " pdb=" C2 NAG N 603 " pdb=" O5 NAG N 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" CA GLU M 67 " pdb=" N GLU M 67 " pdb=" C GLU M 67 " pdb=" CB GLU M 67 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" C2 NAG N 603 " pdb=" C1 NAG N 603 " pdb=" C3 NAG N 603 " pdb=" N2 NAG N 603 " both_signs ideal model delta sigma weight residual False -2.49 -2.64 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2780 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 333 " -0.522 9.50e-02 1.11e+02 2.34e-01 3.36e+01 pdb=" NE ARG N 333 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG N 333 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG N 333 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG N 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 189 " -0.026 2.00e-02 2.50e+03 2.52e-02 7.93e+00 pdb=" CG ASN N 189 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN N 189 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN N 189 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG N 603 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 108 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C VAL H 108 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL H 108 " -0.011 2.00e-02 2.50e+03 pdb=" N SER H 109 " -0.010 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 875 2.72 - 3.27: 14329 3.27 - 3.81: 30007 3.81 - 4.36: 37841 4.36 - 4.90: 56974 Nonbonded interactions: 140026 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.177 3.120 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR C 76 " model vdw 2.190 3.040 nonbonded pdb=" NH1 ARG M 62 " pdb=" OD2 ASP N 416 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG N 333 " pdb=" O2A HEM N 601 " model vdw 2.264 2.496 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.266 3.040 ... (remaining 140021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.005 0.425 17435 Z= 0.159 Angle : 0.590 14.414 24838 Z= 0.321 Chirality : 0.037 0.623 2783 Planarity : 0.007 0.234 2169 Dihedral : 26.624 176.619 7335 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.78 % Allowed : 23.90 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.24), residues: 1293 helix: 1.90 (0.20), residues: 737 sheet: None (None), residues: 0 loop : -0.17 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 185 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE N 332 TRP 0.007 0.001 TRP M 89 HIS 0.002 0.000 HIS M 95 Details of bonding type rmsd covalent geometry : bond 0.00354 (17427) covalent geometry : angle 0.58299 (24826) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.80055 ( 6) hydrogen bonds : bond 0.12352 ( 900) hydrogen bonds : angle 4.69170 ( 2303) Misc. bond : bond 0.24531 ( 3) link_NAG-ASN : bond 0.01147 ( 2) link_NAG-ASN : angle 6.00863 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8352 (tttt) cc_final: 0.7925 (tttm) REVERT: A 115 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8145 (mttp) REVERT: A 129 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7210 (tmt170) REVERT: C 15 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8140 (ptmm) REVERT: D 32 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7286 (pt0) REVERT: E 59 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: E 120 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: F 44 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8435 (tttm) REVERT: G 74 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: G 95 LYS cc_start: 0.8766 (tttt) cc_final: 0.8382 (ttmt) REVERT: G 108 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8610 (mp) REVERT: H 83 ARG cc_start: 0.8451 (mmt-90) cc_final: 0.7996 (mmt90) REVERT: M 27 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8453 (mtp85) REVERT: M 67 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: N 140 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: N 185 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7866 (ttp-110) REVERT: N 210 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7359 (mp) REVERT: N 249 MET cc_start: 0.8813 (mmm) cc_final: 0.8579 (mmt) REVERT: N 462 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7915 (mtt90) REVERT: N 504 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: N 526 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6859 (mp10) outliers start: 31 outliers final: 18 residues processed: 166 average time/residue: 0.7732 time to fit residues: 139.4228 Evaluate side-chains 168 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 547 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.0060 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 75 HIS E 125 GLN G 104 GLN N 467 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121319 restraints weight = 17813.939| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.23 r_work: 0.3343 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.359 17435 Z= 0.174 Angle : 0.571 15.568 24838 Z= 0.314 Chirality : 0.037 0.504 2783 Planarity : 0.004 0.084 2169 Dihedral : 28.840 176.088 4769 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.40 % Allowed : 21.58 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.24), residues: 1293 helix: 2.32 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.26 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 185 TYR 0.010 0.001 TYR D 34 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP N 436 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00397 (17427) covalent geometry : angle 0.56175 (24826) SS BOND : bond 0.00514 ( 3) SS BOND : angle 0.58557 ( 6) hydrogen bonds : bond 0.04813 ( 900) hydrogen bonds : angle 3.34037 ( 2303) Misc. bond : bond 0.20749 ( 3) link_NAG-ASN : bond 0.01714 ( 2) link_NAG-ASN : angle 6.47838 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8023 (tttt) cc_final: 0.7663 (tttm) REVERT: A 120 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8824 (mtt) REVERT: A 129 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7927 (tmt170) REVERT: C 15 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8206 (ptmm) REVERT: D 32 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7277 (pt0) REVERT: F 92 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: G 74 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8345 (mtmm) REVERT: G 92 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: G 95 LYS cc_start: 0.8801 (tttt) cc_final: 0.8553 (ttmt) REVERT: G 108 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8668 (mp) REVERT: H 30 ARG cc_start: 0.7989 (mmt90) cc_final: 0.6810 (mtp-110) REVERT: H 83 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8390 (mmt-90) REVERT: H 90 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: M 27 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8324 (mtp85) REVERT: N 210 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7228 (mp) REVERT: N 249 MET cc_start: 0.8641 (mmm) cc_final: 0.8410 (mmt) REVERT: N 522 MET cc_start: 0.6680 (mtt) cc_final: 0.6086 (mtt) REVERT: N 526 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6797 (mp10) outliers start: 38 outliers final: 13 residues processed: 174 average time/residue: 0.7956 time to fit residues: 150.7050 Evaluate side-chains 163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 53 ARG Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 153 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN N 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123421 restraints weight = 17949.492| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.23 r_work: 0.3369 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.370 17435 Z= 0.136 Angle : 0.553 14.556 24838 Z= 0.305 Chirality : 0.035 0.420 2783 Planarity : 0.004 0.088 2169 Dihedral : 28.830 175.620 4720 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.04 % Allowed : 22.47 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.24), residues: 1293 helix: 2.52 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.20 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 185 TYR 0.009 0.001 TYR D 34 PHE 0.008 0.001 PHE M 86 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00293 (17427) covalent geometry : angle 0.54505 (24826) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.51087 ( 6) hydrogen bonds : bond 0.04271 ( 900) hydrogen bonds : angle 3.19866 ( 2303) Misc. bond : bond 0.21335 ( 3) link_NAG-ASN : bond 0.01401 ( 2) link_NAG-ASN : angle 6.07281 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7923 (tttt) cc_final: 0.7626 (tttm) REVERT: A 129 ARG cc_start: 0.8189 (ttt180) cc_final: 0.7868 (tmt170) REVERT: C 15 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8171 (ptmm) REVERT: D 32 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7269 (pt0) REVERT: E 131 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7341 (mtp85) REVERT: F 92 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: G 74 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8317 (mtmm) REVERT: G 92 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: G 95 LYS cc_start: 0.8788 (tttt) cc_final: 0.8537 (ttmt) REVERT: G 108 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8647 (mp) REVERT: H 83 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.8361 (mmt-90) REVERT: H 90 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: M 27 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8283 (mtp85) REVERT: N 185 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7805 (ttp-110) REVERT: N 210 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7194 (mp) REVERT: N 229 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (mmp-170) REVERT: N 249 MET cc_start: 0.8617 (mmm) cc_final: 0.8383 (mmt) outliers start: 34 outliers final: 12 residues processed: 168 average time/residue: 0.8504 time to fit residues: 155.1383 Evaluate side-chains 163 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121301 restraints weight = 17720.548| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.21 r_work: 0.3340 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.340 17435 Z= 0.180 Angle : 0.567 15.736 24838 Z= 0.310 Chirality : 0.036 0.394 2783 Planarity : 0.004 0.099 2169 Dihedral : 28.851 176.237 4712 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.94 % Allowed : 20.95 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.24), residues: 1293 helix: 2.49 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 185 TYR 0.011 0.001 TYR D 34 PHE 0.008 0.001 PHE B 61 TRP 0.007 0.001 TRP N 436 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00416 (17427) covalent geometry : angle 0.55967 (24826) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.58812 ( 6) hydrogen bonds : bond 0.04681 ( 900) hydrogen bonds : angle 3.17205 ( 2303) Misc. bond : bond 0.19649 ( 3) link_NAG-ASN : bond 0.01298 ( 2) link_NAG-ASN : angle 5.76496 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7938 (tttt) cc_final: 0.7559 (tttm) REVERT: A 129 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7932 (tmt170) REVERT: C 15 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8181 (ptmm) REVERT: D 32 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7283 (pt0) REVERT: E 131 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: G 74 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8310 (mtmm) REVERT: G 92 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: G 95 LYS cc_start: 0.8802 (tttt) cc_final: 0.8551 (ttmt) REVERT: G 108 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8644 (mp) REVERT: H 83 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8382 (mmt-90) REVERT: H 90 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: M 27 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8233 (mtp85) REVERT: M 52 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7400 (mttp) REVERT: N 185 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7785 (ttp-110) REVERT: N 192 ASN cc_start: 0.7667 (m-40) cc_final: 0.7407 (m-40) REVERT: N 210 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7132 (mp) REVERT: N 249 MET cc_start: 0.8618 (mmm) cc_final: 0.8386 (mmt) REVERT: N 526 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: N 530 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8248 (mt0) outliers start: 44 outliers final: 19 residues processed: 175 average time/residue: 0.7425 time to fit residues: 141.2236 Evaluate side-chains 167 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN E 125 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121811 restraints weight = 17736.128| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.21 r_work: 0.3345 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.339 17435 Z= 0.160 Angle : 0.564 15.636 24838 Z= 0.309 Chirality : 0.036 0.384 2783 Planarity : 0.004 0.095 2169 Dihedral : 28.856 176.282 4712 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.40 % Allowed : 21.58 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.24), residues: 1293 helix: 2.53 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.32 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 202 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP N 436 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00362 (17427) covalent geometry : angle 0.55736 (24826) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.65839 ( 6) hydrogen bonds : bond 0.04554 ( 900) hydrogen bonds : angle 3.16298 ( 2303) Misc. bond : bond 0.19589 ( 3) link_NAG-ASN : bond 0.01291 ( 2) link_NAG-ASN : angle 5.70807 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7915 (tttt) cc_final: 0.7534 (tttm) REVERT: A 129 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7918 (tmt170) REVERT: C 15 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8190 (ptmm) REVERT: D 32 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7294 (pt0) REVERT: E 59 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: E 64 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8256 (mttm) REVERT: E 131 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7359 (mtp85) REVERT: F 92 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7998 (ttp80) REVERT: G 74 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8314 (mtmm) REVERT: G 92 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: G 95 LYS cc_start: 0.8797 (tttt) cc_final: 0.8547 (ttmt) REVERT: G 108 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8650 (mp) REVERT: H 83 ARG cc_start: 0.8595 (mmt-90) cc_final: 0.8376 (mmt-90) REVERT: H 90 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: M 27 ARG cc_start: 0.8815 (mmm160) cc_final: 0.8253 (mtp85) REVERT: M 52 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7417 (mttp) REVERT: N 185 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7707 (ttp-110) REVERT: N 192 ASN cc_start: 0.7669 (m-40) cc_final: 0.7434 (m-40) REVERT: N 210 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7216 (mp) REVERT: N 249 MET cc_start: 0.8633 (mmm) cc_final: 0.8401 (mmt) REVERT: N 526 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: N 530 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8270 (mt0) outliers start: 38 outliers final: 18 residues processed: 165 average time/residue: 0.8205 time to fit residues: 146.5853 Evaluate side-chains 169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121723 restraints weight = 17713.773| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.22 r_work: 0.3348 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.343 17435 Z= 0.169 Angle : 0.564 15.527 24838 Z= 0.309 Chirality : 0.036 0.383 2783 Planarity : 0.004 0.097 2169 Dihedral : 28.859 176.053 4712 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.49 % Allowed : 21.84 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.24), residues: 1293 helix: 2.50 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.34 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 202 TYR 0.010 0.001 TYR D 34 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP N 436 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00387 (17427) covalent geometry : angle 0.55737 (24826) SS BOND : bond 0.00355 ( 3) SS BOND : angle 1.02655 ( 6) hydrogen bonds : bond 0.04579 ( 900) hydrogen bonds : angle 3.15718 ( 2303) Misc. bond : bond 0.19825 ( 3) link_NAG-ASN : bond 0.01110 ( 2) link_NAG-ASN : angle 5.61167 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7915 (tttt) cc_final: 0.7536 (tttm) REVERT: A 129 ARG cc_start: 0.8185 (ttt180) cc_final: 0.7928 (tmt170) REVERT: C 15 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8177 (ptmm) REVERT: D 32 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7298 (pt0) REVERT: E 59 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8051 (pt0) REVERT: E 64 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: E 131 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7416 (mtp85) REVERT: F 92 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8004 (ttp80) REVERT: G 74 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8289 (mtmm) REVERT: G 92 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: G 95 LYS cc_start: 0.8795 (tttt) cc_final: 0.8547 (ttmt) REVERT: G 108 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8638 (mp) REVERT: H 83 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.8380 (mmt-90) REVERT: H 90 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: M 27 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8234 (mtp85) REVERT: M 52 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7428 (mttp) REVERT: N 185 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7733 (ttp-110) REVERT: N 192 ASN cc_start: 0.7673 (m-40) cc_final: 0.7464 (m-40) REVERT: N 210 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7156 (mp) REVERT: N 249 MET cc_start: 0.8625 (mmm) cc_final: 0.8396 (mmt) REVERT: N 526 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: N 530 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8242 (mt0) outliers start: 39 outliers final: 21 residues processed: 167 average time/residue: 0.7787 time to fit residues: 141.0098 Evaluate side-chains 172 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 118 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 47 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.159469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122496 restraints weight = 17694.638| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.21 r_work: 0.3357 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 17435 Z= 0.140 Angle : 0.555 15.461 24838 Z= 0.305 Chirality : 0.035 0.370 2783 Planarity : 0.004 0.091 2169 Dihedral : 28.856 176.247 4712 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.22 % Allowed : 22.38 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.24), residues: 1293 helix: 2.57 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 202 TYR 0.009 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP N 436 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00302 (17427) covalent geometry : angle 0.54879 (24826) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.41467 ( 6) hydrogen bonds : bond 0.04362 ( 900) hydrogen bonds : angle 3.14137 ( 2303) Misc. bond : bond 0.19754 ( 3) link_NAG-ASN : bond 0.01163 ( 2) link_NAG-ASN : angle 5.56769 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7893 (tttt) cc_final: 0.7608 (tttm) REVERT: A 129 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7936 (tmt170) REVERT: C 15 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8169 (ptmm) REVERT: D 32 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7305 (pt0) REVERT: E 59 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: E 64 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (mttm) REVERT: E 131 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7358 (mtp85) REVERT: F 92 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: G 74 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8286 (mtmm) REVERT: G 92 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: G 95 LYS cc_start: 0.8777 (tttt) cc_final: 0.8534 (ttmt) REVERT: G 108 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8670 (mp) REVERT: H 83 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8372 (mmt-90) REVERT: H 90 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: M 27 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8215 (mtp85) REVERT: M 52 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7431 (mttp) REVERT: N 185 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7709 (ttp-110) REVERT: N 192 ASN cc_start: 0.7664 (m-40) cc_final: 0.7435 (m-40) REVERT: N 210 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7137 (mp) REVERT: N 229 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7342 (mmp-170) REVERT: N 249 MET cc_start: 0.8599 (mmm) cc_final: 0.8364 (mmt) REVERT: N 526 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6851 (mp10) REVERT: N 530 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8247 (mt0) outliers start: 36 outliers final: 18 residues processed: 165 average time/residue: 0.8206 time to fit residues: 146.9310 Evaluate side-chains 169 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 522 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.157539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120375 restraints weight = 17823.331| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.21 r_work: 0.3327 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.323 17435 Z= 0.191 Angle : 0.574 15.242 24838 Z= 0.316 Chirality : 0.037 0.384 2783 Planarity : 0.004 0.102 2169 Dihedral : 28.950 176.363 4712 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.86 % Allowed : 22.83 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.24), residues: 1293 helix: 2.43 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.40 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 307 TYR 0.012 0.001 TYR D 34 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP M 89 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00442 (17427) covalent geometry : angle 0.56780 (24826) SS BOND : bond 0.00364 ( 3) SS BOND : angle 0.69167 ( 6) hydrogen bonds : bond 0.04880 ( 900) hydrogen bonds : angle 3.19258 ( 2303) Misc. bond : bond 0.18665 ( 3) link_NAG-ASN : bond 0.01094 ( 2) link_NAG-ASN : angle 5.56381 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7941 (tttt) cc_final: 0.7563 (tttm) REVERT: A 129 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7870 (tmt170) REVERT: C 15 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8128 (ptmm) REVERT: D 32 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7315 (pt0) REVERT: E 59 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: E 131 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7415 (mtp85) REVERT: F 92 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7982 (ttp80) REVERT: G 74 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8286 (mtmm) REVERT: G 95 LYS cc_start: 0.8782 (tttt) cc_final: 0.8542 (ttmt) REVERT: G 108 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8667 (mp) REVERT: H 30 ARG cc_start: 0.8021 (mmt90) cc_final: 0.6782 (mtp-110) REVERT: H 83 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8223 (mmt90) REVERT: H 90 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: M 27 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8148 (mtp85) REVERT: M 52 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7487 (mttp) REVERT: N 185 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7691 (ttp-110) REVERT: N 192 ASN cc_start: 0.7682 (m-40) cc_final: 0.7462 (m-40) REVERT: N 210 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7098 (mp) REVERT: N 526 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6803 (mp10) outliers start: 32 outliers final: 17 residues processed: 157 average time/residue: 0.8057 time to fit residues: 137.0858 Evaluate side-chains 158 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN E 125 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121058 restraints weight = 17706.020| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.21 r_work: 0.3337 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.321 17435 Z= 0.153 Angle : 0.571 15.323 24838 Z= 0.314 Chirality : 0.035 0.376 2783 Planarity : 0.004 0.096 2169 Dihedral : 28.946 176.579 4710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.78 % Allowed : 22.83 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.24), residues: 1293 helix: 2.44 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.41 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 307 TYR 0.011 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.010 0.001 TRP M 89 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00341 (17427) covalent geometry : angle 0.56483 (24826) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.66402 ( 6) hydrogen bonds : bond 0.04615 ( 900) hydrogen bonds : angle 3.17627 ( 2303) Misc. bond : bond 0.18518 ( 3) link_NAG-ASN : bond 0.01170 ( 2) link_NAG-ASN : angle 5.46629 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8191 (ttt180) cc_final: 0.7866 (tmt170) REVERT: C 15 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8118 (ptmm) REVERT: D 32 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7307 (pt0) REVERT: E 59 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: E 64 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8285 (mttm) REVERT: E 131 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7355 (mtp85) REVERT: F 92 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: G 36 LYS cc_start: 0.8712 (mttp) cc_final: 0.8497 (mmmm) REVERT: G 74 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8280 (mtmm) REVERT: G 95 LYS cc_start: 0.8774 (tttt) cc_final: 0.8539 (ttmt) REVERT: G 108 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (mp) REVERT: H 83 ARG cc_start: 0.8619 (mmt-90) cc_final: 0.8210 (mmt90) REVERT: H 90 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: M 27 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8149 (mtp85) REVERT: M 52 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7481 (mttp) REVERT: N 185 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7696 (ttp-110) REVERT: N 192 ASN cc_start: 0.7674 (m-40) cc_final: 0.7458 (m-40) REVERT: N 210 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7102 (mp) REVERT: N 259 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7198 (ttp-170) REVERT: N 526 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6796 (mp10) outliers start: 31 outliers final: 18 residues processed: 155 average time/residue: 0.7688 time to fit residues: 129.2372 Evaluate side-chains 161 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 259 ARG Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 0.0050 chunk 114 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121446 restraints weight = 17723.681| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.22 r_work: 0.3342 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.325 17435 Z= 0.145 Angle : 0.567 15.202 24838 Z= 0.312 Chirality : 0.035 0.369 2783 Planarity : 0.004 0.093 2169 Dihedral : 28.938 176.472 4710 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.69 % Allowed : 23.10 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.24), residues: 1293 helix: 2.48 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.39 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 307 TYR 0.010 0.001 TYR D 34 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP M 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00320 (17427) covalent geometry : angle 0.56132 (24826) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.60651 ( 6) hydrogen bonds : bond 0.04516 ( 900) hydrogen bonds : angle 3.16197 ( 2303) Misc. bond : bond 0.18773 ( 3) link_NAG-ASN : bond 0.01215 ( 2) link_NAG-ASN : angle 5.38206 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8196 (ttt180) cc_final: 0.7865 (tmt170) REVERT: C 15 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8120 (ptmm) REVERT: D 32 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7301 (pt0) REVERT: E 59 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: E 64 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (mttm) REVERT: E 131 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7356 (mtp85) REVERT: F 92 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7995 (ttp80) REVERT: G 36 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8493 (mmmm) REVERT: G 74 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8280 (mtmm) REVERT: G 95 LYS cc_start: 0.8774 (tttt) cc_final: 0.8536 (ttmt) REVERT: G 108 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8658 (mp) REVERT: H 83 ARG cc_start: 0.8607 (mmt-90) cc_final: 0.8313 (mmt90) REVERT: H 90 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: M 27 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8123 (mtp85) REVERT: M 52 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7476 (mttp) REVERT: N 185 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7692 (ttp-110) REVERT: N 192 ASN cc_start: 0.7647 (m-40) cc_final: 0.7424 (m-40) REVERT: N 210 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7073 (mp) REVERT: N 249 MET cc_start: 0.8626 (mmm) cc_final: 0.8385 (mmt) REVERT: N 526 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6790 (mp10) outliers start: 30 outliers final: 16 residues processed: 154 average time/residue: 0.8164 time to fit residues: 136.4612 Evaluate side-chains 161 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 287 MET Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 314 ARG Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 333 ARG Chi-restraints excluded: chain N residue 453 THR Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 553 MET Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119341 restraints weight = 17704.557| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.21 r_work: 0.3310 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 17435 Z= 0.219 Angle : 0.596 16.107 24838 Z= 0.326 Chirality : 0.038 0.393 2783 Planarity : 0.005 0.104 2169 Dihedral : 29.008 176.860 4710 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.51 % Allowed : 23.28 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.24), residues: 1293 helix: 2.29 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.51 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 202 TYR 0.012 0.001 TYR D 34 PHE 0.009 0.001 PHE N 503 TRP 0.008 0.001 TRP M 89 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00514 (17427) covalent geometry : angle 0.59020 (24826) SS BOND : bond 0.00377 ( 3) SS BOND : angle 0.74694 ( 6) hydrogen bonds : bond 0.05191 ( 900) hydrogen bonds : angle 3.22656 ( 2303) Misc. bond : bond 0.18957 ( 3) link_NAG-ASN : bond 0.00985 ( 2) link_NAG-ASN : angle 5.51153 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.79 seconds wall clock time: 92 minutes 29.94 seconds (5549.94 seconds total)