Starting phenix.real_space_refine on Fri Feb 16 19:25:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enn_31217/02_2024/7enn_31217_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 294 5.49 5 S 31 5.16 5 Be 1 3.05 5 C 9365 2.51 5 N 2989 2.21 5 O 3636 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 30": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K ARG 145": "NH1" <-> "NH2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 174": "OD1" <-> "OD2" Residue "K TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 353": "OD1" <-> "OD2" Residue "K GLU 391": "OE1" <-> "OE2" Residue "K ASP 440": "OD1" <-> "OD2" Residue "K ASP 448": "OD1" <-> "OD2" Residue "K ARG 454": "NH1" <-> "NH2" Residue "K ARG 457": "NH1" <-> "NH2" Residue "K ARG 472": "NH1" <-> "NH2" Residue "K ASP 473": "OD1" <-> "OD2" Residue "K ARG 481": "NH1" <-> "NH2" Residue "K PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 539": "OE1" <-> "OE2" Residue "K GLU 567": "OE1" <-> "OE2" Residue "K PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 579": "OD1" <-> "OD2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 614": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 23": "NH1" <-> "NH2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L ASP 68": "OD1" <-> "OD2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4315 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 14, 'TRANS': 524} Chain breaks: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.44, per 1000 atoms: 0.52 Number of scatterers: 16319 At special positions: 0 Unit cell: (143.431, 126.652, 115.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 294 15.00 F 3 9.00 O 3636 8.00 N 2989 7.00 C 9365 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.19 Conformation dependent library (CDL) restraints added in 2.0 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 2 sheets defined 56.5% alpha, 3.8% beta 145 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'K' and resid 33 through 39 Processing helix chain 'K' and resid 48 through 61 Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 104 through 117 removed outlier: 3.565A pdb=" N LEU K 107 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER K 108 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K 114 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE K 117 " --> pdb=" O MET K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 137 Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'K' and resid 162 through 164 No H-bonds generated for 'chain 'K' and resid 162 through 164' Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 185 through 191 Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 210 through 220 Processing helix chain 'K' and resid 227 through 237 removed outlier: 3.713A pdb=" N VAL K 230 " --> pdb=" O LYS K 227 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY K 231 " --> pdb=" O GLU K 228 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG K 236 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 253 removed outlier: 3.867A pdb=" N GLU K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 295 Processing helix chain 'K' and resid 314 through 323 Processing helix chain 'K' and resid 325 through 327 No H-bonds generated for 'chain 'K' and resid 325 through 327' Processing helix chain 'K' and resid 329 through 331 No H-bonds generated for 'chain 'K' and resid 329 through 331' Processing helix chain 'K' and resid 341 through 344 No H-bonds generated for 'chain 'K' and resid 341 through 344' Processing helix chain 'K' and resid 347 through 362 Processing helix chain 'K' and resid 373 through 386 Processing helix chain 'K' and resid 400 through 411 removed outlier: 3.758A pdb=" N GLY K 410 " --> pdb=" O ILE K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 424 No H-bonds generated for 'chain 'K' and resid 421 through 424' Processing helix chain 'K' and resid 445 through 454 Processing helix chain 'K' and resid 475 through 497 removed outlier: 4.000A pdb=" N LEU K 489 " --> pdb=" O SER K 485 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR K 490 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN K 491 " --> pdb=" O LEU K 487 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET K 492 " --> pdb=" O GLN K 488 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 526 No H-bonds generated for 'chain 'K' and resid 523 through 526' Processing helix chain 'K' and resid 536 through 544 removed outlier: 4.090A pdb=" N LEU K 542 " --> pdb=" O GLU K 539 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU K 544 " --> pdb=" O ILE K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 587 through 598 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.101A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 50 through 75 Processing helix chain 'L' and resid 83 through 93 removed outlier: 3.560A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 73 removed outlier: 3.552A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.761A pdb=" N LYS D 105 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.559A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 120 Processing sheet with id= A, first strand: chain 'K' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'K' and resid 571 through 573 removed outlier: 7.036A pdb=" N VAL K 464 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL K 276 " --> pdb=" O VAL K 464 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL K 466 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE K 278 " --> pdb=" O VAL K 466 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG K 468 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS K 280 " --> pdb=" O ARG K 468 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE K 470 " --> pdb=" O HIS K 280 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER K 420 " --> pdb=" O VAL K 393 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 4922 1.45 - 1.57: 8170 1.57 - 1.69: 586 1.69 - 1.81: 54 Bond restraints: 17205 Sorted by residual: bond pdb=" BE BEF K 902 " pdb=" F2 BEF K 902 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" BE BEF K 902 " pdb=" F1 BEF K 902 " ideal model delta sigma weight residual 1.476 1.700 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CA GLN K 207 " pdb=" C GLN K 207 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.90e+00 bond pdb=" CA GLU K 334 " pdb=" CB GLU K 334 " ideal model delta sigma weight residual 1.525 1.538 -0.014 8.30e-03 1.45e+04 2.75e+00 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.69: 1610 105.69 - 113.41: 9733 113.41 - 121.13: 8818 121.13 - 128.85: 4073 128.85 - 136.56: 250 Bond angle restraints: 24484 Sorted by residual: angle pdb=" F1 BEF K 902 " pdb=" BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 120.12 99.06 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F2 BEF K 902 " pdb=" BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 119.96 105.13 14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C VAL K 397 " pdb=" N ARG K 398 " pdb=" CA ARG K 398 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N LEU K 522 " pdb=" CA LEU K 522 " pdb=" C LEU K 522 " ideal model delta sigma weight residual 111.81 106.27 5.54 1.54e+00 4.22e-01 1.29e+01 angle pdb=" C PRO K 333 " pdb=" N GLU K 334 " pdb=" CA GLU K 334 " ideal model delta sigma weight residual 124.21 128.50 -4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 24479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8134 35.15 - 70.31: 1435 70.31 - 105.46: 9 105.46 - 140.61: 3 140.61 - 175.77: 3 Dihedral angle restraints: 9584 sinusoidal: 5825 harmonic: 3759 Sorted by residual: dihedral pdb=" C5' ADP K 901 " pdb=" O5' ADP K 901 " pdb=" PA ADP K 901 " pdb=" O2A ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.77 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PA ADP K 901 " pdb=" PB ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.01 -125.01 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PB ADP K 901 " pdb=" PA ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 58.31 -118.31 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1879 0.036 - 0.072: 725 0.072 - 0.108: 142 0.108 - 0.144: 23 0.144 - 0.180: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CB ILE H 91 " pdb=" CA ILE H 91 " pdb=" CG1 ILE H 91 " pdb=" CG2 ILE H 91 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CB VAL K 596 " pdb=" CA VAL K 596 " pdb=" CG1 VAL K 596 " pdb=" CG2 VAL K 596 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C3' ADP K 901 " pdb=" C2' ADP K 901 " pdb=" C4' ADP K 901 " pdb=" O3' ADP K 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2769 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 444 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO K 445 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 445 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 445 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 168 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP K 168 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP K 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP K 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 168 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 168 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 517 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE K 517 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE K 517 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU K 518 " 0.011 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 454 2.68 - 3.24: 14251 3.24 - 3.79: 28761 3.79 - 4.35: 38842 4.35 - 4.90: 56778 Nonbonded interactions: 139086 Sorted by model distance: nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.127 2.496 nonbonded pdb=" OH TYR K 153 " pdb=" O ASP K 174 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR K 214 " pdb=" O SER K 226 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.190 2.440 nonbonded pdb=" O SER K 244 " pdb=" OG SER K 248 " model vdw 2.205 2.440 ... (remaining 139081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'F' and resid 23 through 101) selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.620 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 53.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.006 0.229 17205 Z= 0.329 Angle : 0.683 21.061 24484 Z= 0.403 Chirality : 0.038 0.180 2772 Planarity : 0.004 0.049 2097 Dihedral : 25.221 175.768 7160 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1274 helix: 1.02 (0.18), residues: 789 sheet: -0.83 (0.64), residues: 80 loop : -2.24 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 168 HIS 0.003 0.001 HIS L 75 PHE 0.015 0.002 PHE K 409 TYR 0.023 0.002 TYR G 50 ARG 0.013 0.001 ARG K 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 2.0592 time to fit residues: 452.7822 Evaluate side-chains 161 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 429 ASN K 447 ASN K 488 GLN K 491 ASN L 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 46 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17205 Z= 0.209 Angle : 0.587 10.055 24484 Z= 0.340 Chirality : 0.036 0.143 2772 Planarity : 0.004 0.042 2097 Dihedral : 28.837 168.989 4627 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 1.46 % Allowed : 10.16 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1274 helix: 1.33 (0.19), residues: 788 sheet: -0.19 (0.67), residues: 75 loop : -2.02 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 39 HIS 0.003 0.001 HIS K 147 PHE 0.020 0.001 PHE K 409 TYR 0.012 0.001 TYR K 214 ARG 0.006 0.000 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: K 374 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8094 (mm-40) REVERT: K 572 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.4178 (tmm) REVERT: A 120 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8538 (mtt) REVERT: E 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: H 43 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8706 (mmtm) REVERT: H 105 LYS cc_start: 0.8154 (mtpm) cc_final: 0.7910 (mttp) outliers start: 16 outliers final: 6 residues processed: 178 average time/residue: 1.9368 time to fit residues: 370.6880 Evaluate side-chains 173 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 572 MET Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 429 ASN K 447 ASN K 488 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 17205 Z= 0.397 Angle : 0.628 10.140 24484 Z= 0.361 Chirality : 0.040 0.142 2772 Planarity : 0.004 0.051 2097 Dihedral : 28.975 167.512 4627 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.74 % Allowed : 10.06 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1274 helix: 1.28 (0.19), residues: 789 sheet: -0.54 (0.63), residues: 80 loop : -1.94 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 110 HIS 0.003 0.001 HIS D 46 PHE 0.029 0.002 PHE K 409 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.001 ARG K 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.565 Fit side-chains REVERT: K 374 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: C 92 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: E 59 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: G 64 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: H 43 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8671 (mmtm) outliers start: 30 outliers final: 13 residues processed: 178 average time/residue: 1.9322 time to fit residues: 368.6344 Evaluate side-chains 179 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17205 Z= 0.220 Angle : 0.600 10.848 24484 Z= 0.346 Chirality : 0.036 0.138 2772 Planarity : 0.004 0.041 2097 Dihedral : 28.966 166.548 4627 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.20 % Allowed : 11.62 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1274 helix: 1.41 (0.19), residues: 788 sheet: -0.46 (0.63), residues: 80 loop : -1.86 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 39 HIS 0.003 0.001 HIS L 75 PHE 0.021 0.001 PHE K 409 TYR 0.013 0.001 TYR K 214 ARG 0.007 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.563 Fit side-chains REVERT: K 374 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: C 64 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: C 92 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: E 59 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7745 (pm20) outliers start: 24 outliers final: 14 residues processed: 179 average time/residue: 1.8858 time to fit residues: 362.6331 Evaluate side-chains 185 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17205 Z= 0.281 Angle : 0.583 9.250 24484 Z= 0.338 Chirality : 0.037 0.137 2772 Planarity : 0.004 0.043 2097 Dihedral : 28.797 158.348 4627 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.56 % Allowed : 12.35 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1274 helix: 1.57 (0.19), residues: 781 sheet: -0.32 (0.64), residues: 78 loop : -1.69 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 39 HIS 0.002 0.001 HIS K 147 PHE 0.022 0.001 PHE K 409 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.450 Fit side-chains REVERT: K 374 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8010 (mm-40) REVERT: C 64 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: C 92 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: E 59 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: G 64 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: H 32 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7673 (pt0) outliers start: 28 outliers final: 16 residues processed: 178 average time/residue: 1.8317 time to fit residues: 351.0405 Evaluate side-chains 183 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17205 Z= 0.168 Angle : 0.571 8.987 24484 Z= 0.332 Chirality : 0.035 0.139 2772 Planarity : 0.004 0.039 2097 Dihedral : 28.795 156.829 4627 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.29 % Allowed : 12.72 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.24), residues: 1274 helix: 1.72 (0.19), residues: 781 sheet: -0.32 (0.63), residues: 78 loop : -1.58 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 39 HIS 0.002 0.001 HIS L 75 PHE 0.016 0.001 PHE K 409 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: K 374 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7975 (mm-40) REVERT: C 64 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: C 92 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: E 59 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: H 32 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7652 (pt0) outliers start: 25 outliers final: 15 residues processed: 175 average time/residue: 1.7862 time to fit residues: 337.1035 Evaluate side-chains 179 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 447 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17205 Z= 0.204 Angle : 0.563 8.656 24484 Z= 0.327 Chirality : 0.035 0.142 2772 Planarity : 0.004 0.040 2097 Dihedral : 28.734 156.107 4627 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 2.29 % Allowed : 13.08 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1274 helix: 1.75 (0.19), residues: 781 sheet: -0.27 (0.62), residues: 78 loop : -1.52 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 39 HIS 0.002 0.000 HIS L 75 PHE 0.014 0.001 PHE K 409 TYR 0.010 0.001 TYR L 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.446 Fit side-chains REVERT: K 374 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: C 64 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: C 92 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: E 59 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: G 64 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: H 32 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7659 (pt0) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 1.8774 time to fit residues: 341.3428 Evaluate side-chains 179 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.0270 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17205 Z= 0.172 Angle : 0.563 8.535 24484 Z= 0.327 Chirality : 0.034 0.139 2772 Planarity : 0.004 0.043 2097 Dihedral : 28.726 155.264 4627 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 2.01 % Allowed : 13.72 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1274 helix: 1.81 (0.19), residues: 781 sheet: -0.28 (0.61), residues: 78 loop : -1.48 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 39 HIS 0.002 0.000 HIS L 75 PHE 0.012 0.001 PHE K 409 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: K 374 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: C 64 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: C 92 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: E 59 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: H 32 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7652 (pt0) outliers start: 22 outliers final: 15 residues processed: 172 average time/residue: 1.9015 time to fit residues: 352.3204 Evaluate side-chains 179 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 447 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17205 Z= 0.325 Angle : 0.596 9.034 24484 Z= 0.342 Chirality : 0.037 0.140 2772 Planarity : 0.004 0.046 2097 Dihedral : 28.757 149.316 4627 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.92 % Allowed : 14.00 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1274 helix: 1.70 (0.19), residues: 781 sheet: -0.23 (0.62), residues: 78 loop : -1.52 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 39 HIS 0.002 0.001 HIS L 75 PHE 0.021 0.001 PHE K 409 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG K 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: K 374 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8012 (mm-40) REVERT: C 64 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: C 92 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: E 59 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: G 64 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: H 32 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: H 105 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8127 (mttt) outliers start: 21 outliers final: 13 residues processed: 171 average time/residue: 1.8574 time to fit residues: 341.4092 Evaluate side-chains 178 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17205 Z= 0.242 Angle : 0.591 8.970 24484 Z= 0.339 Chirality : 0.036 0.225 2772 Planarity : 0.004 0.046 2097 Dihedral : 28.767 149.641 4627 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.20 % Allowed : 14.09 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1274 helix: 1.74 (0.19), residues: 781 sheet: -0.22 (0.62), residues: 78 loop : -1.50 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 39 HIS 0.002 0.001 HIS L 75 PHE 0.019 0.001 PHE K 409 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: K 374 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: C 64 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: C 92 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: E 59 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: G 64 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: H 32 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: H 105 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8110 (mttt) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 1.8140 time to fit residues: 329.5460 Evaluate side-chains 182 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088308 restraints weight = 23532.282| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.46 r_work: 0.2990 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17205 Z= 0.248 Angle : 0.584 8.772 24484 Z= 0.336 Chirality : 0.036 0.250 2772 Planarity : 0.004 0.040 2097 Dihedral : 28.747 150.053 4627 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.01 % Allowed : 14.27 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1274 helix: 1.74 (0.19), residues: 781 sheet: -0.16 (0.62), residues: 78 loop : -1.47 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 39 HIS 0.004 0.001 HIS H 46 PHE 0.016 0.001 PHE K 409 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.72 seconds wall clock time: 112 minutes 10.29 seconds (6730.29 seconds total)