Starting phenix.real_space_refine on Fri Feb 16 18:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3w_32995/02_2024/7x3w_32995_updated.pdb" } resolution = 3.1 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9257 2.51 5 N 2959 2.21 5 O 3594 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 221": "OD1" <-> "OD2" Residue "K TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K ARG 308": "NH1" <-> "NH2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 388": "OE1" <-> "OE2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 614": "NH1" <-> "NH2" Residue "K ARG 639": "NH1" <-> "NH2" Residue "K ARG 645": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16134 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 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: "B" 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: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 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: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 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: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 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: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4129 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.99, per 1000 atoms: 0.50 Number of scatterers: 16134 At special positions: 0 Unit cell: (109.332, 127.735, 150.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3594 8.00 N 2959 7.00 C 9257 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 3 sheets defined 57.8% alpha, 2.8% beta 144 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 8.79 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.042A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 72 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: 3.657A pdb=" N LYS D 105 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.064A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 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 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 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 helix chain 'K' and resid 102 through 112 removed outlier: 3.687A pdb=" N HIS K 111 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 124 Processing helix chain 'K' and resid 132 through 142 removed outlier: 3.797A pdb=" N ASP K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL K 139 " --> pdb=" O VAL K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 213 Processing helix chain 'K' and resid 227 through 240 Processing helix chain 'K' and resid 254 through 267 removed outlier: 3.501A pdb=" N LEU K 257 " --> pdb=" O LYS K 254 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN K 258 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP K 260 " --> pdb=" O LEU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 289 removed outlier: 3.568A pdb=" N LEU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 308 removed outlier: 4.213A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 314 Processing helix chain 'K' and resid 328 through 330 No H-bonds generated for 'chain 'K' and resid 328 through 330' Processing helix chain 'K' and resid 335 through 340 Processing helix chain 'K' and resid 360 through 369 removed outlier: 4.635A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 375 No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 379 through 389 removed outlier: 3.602A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLU K 388 " --> pdb=" O TRP K 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 406 removed outlier: 3.639A pdb=" N GLN K 406 " --> pdb=" O THR K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 445 removed outlier: 4.117A pdb=" N LYS K 439 " --> pdb=" O SER K 435 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 477 Processing helix chain 'K' and resid 479 through 482 removed outlier: 3.519A pdb=" N PHE K 482 " --> pdb=" O PRO K 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 479 through 482' Processing helix chain 'K' and resid 495 through 500 Processing helix chain 'K' and resid 502 through 517 removed outlier: 4.463A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 541 Processing helix chain 'K' and resid 555 through 565 Processing helix chain 'K' and resid 602 through 611 removed outlier: 4.258A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 656 removed outlier: 3.726A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG K 655 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR K 656 " --> pdb=" O GLN K 652 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 320 through 323 Processing sheet with id= B, first strand: chain 'K' and resid 424 through 432 removed outlier: 6.248A pdb=" N VAL K 621 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU K 427 " --> pdb=" O VAL K 621 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL K 623 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU K 429 " --> pdb=" O VAL K 623 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG K 625 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL K 431 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL K 627 " --> pdb=" O VAL K 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'K' and resid 592 through 595 492 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 7.95 Time building geometry restraints manager: 8.19 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: 2845 1.33 - 1.45: 5316 1.45 - 1.57: 8227 1.57 - 1.69: 585 1.69 - 1.81: 46 Bond restraints: 17019 Sorted by residual: bond pdb=" BE BEF K1202 " pdb=" F2 BEF K1202 " ideal model delta sigma weight residual 1.476 1.706 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" BE BEF K1202 " pdb=" F1 BEF K1202 " ideal model delta sigma weight residual 1.476 1.704 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 1.476 1.691 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CA ARG F 95 " pdb=" CB ARG F 95 " ideal model delta sigma weight residual 1.528 1.473 0.056 2.61e-02 1.47e+03 4.57e+00 bond pdb=" CG LEU E 82 " pdb=" CD2 LEU E 82 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.12e+00 ... (remaining 17014 not shown) Histogram of bond angle deviations from ideal: 97.53 - 105.26: 1388 105.26 - 112.98: 9742 112.98 - 120.70: 7856 120.70 - 128.42: 4930 128.42 - 136.14: 334 Bond angle restraints: 24250 Sorted by residual: angle pdb=" F1 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 120.12 99.61 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" F2 BEF K1202 " pdb=" BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 119.96 104.96 15.00 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C LEU K 340 " pdb=" N ARG K 341 " pdb=" CA ARG K 341 " ideal model delta sigma weight residual 121.94 115.15 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA MET K 433 " pdb=" CB MET K 433 " pdb=" CG MET K 433 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.68e+00 ... (remaining 24245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 7842 31.84 - 63.67: 1626 63.67 - 95.51: 37 95.51 - 127.34: 0 127.34 - 159.18: 4 Dihedral angle restraints: 9509 sinusoidal: 5817 harmonic: 3692 Sorted by residual: dihedral pdb=" C5' ADP K1201 " pdb=" O5' ADP K1201 " pdb=" PA ADP K1201 " pdb=" O2A ADP K1201 " ideal model delta sinusoidal sigma weight residual 300.00 160.16 139.84 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O1B ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PB ADP K1201 " pdb=" PA ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 -153.84 93.84 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" CA ASN K 359 " pdb=" C ASN K 359 " pdb=" N LEU K 360 " pdb=" CA LEU K 360 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1354 0.031 - 0.061: 913 0.061 - 0.092: 366 0.092 - 0.123: 92 0.123 - 0.153: 28 Chirality restraints: 2753 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CB ILE K 558 " pdb=" CA ILE K 558 " pdb=" CG1 ILE K 558 " pdb=" CG2 ILE K 558 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2750 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.021 2.00e-02 2.50e+03 2.57e-02 1.33e+01 pdb=" CG TYR B 88 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.026 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR D 80 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO H 100 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.034 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 58 2.45 - 3.06: 10381 3.06 - 3.67: 26107 3.67 - 4.29: 41523 4.29 - 4.90: 60548 Nonbonded interactions: 138617 Sorted by model distance: nonbonded pdb=" O3B ADP K1201 " pdb="MG MG K1203 " model vdw 1.833 2.170 nonbonded pdb=" N LYS K 227 " pdb="MG MG K1203 " model vdw 1.946 2.250 nonbonded pdb=" N THR K 228 " pdb="MG MG K1203 " model vdw 2.010 2.250 nonbonded pdb=" NZ LYS K 314 " pdb=" O GLU K 342 " model vdw 2.104 2.520 nonbonded pdb=" OG1 THR K 228 " pdb=" O3B ADP K1201 " model vdw 2.124 2.440 ... (remaining 138612 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 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } 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)) } 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: 2.500 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: 10.150 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 51.730 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.009 0.230 17019 Z= 0.580 Angle : 0.771 20.515 24250 Z= 0.439 Chirality : 0.046 0.153 2753 Planarity : 0.004 0.061 2063 Dihedral : 25.400 159.177 7117 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.00 (0.24), residues: 1241 helix: 1.11 (0.19), residues: 782 sheet: -1.75 (0.68), residues: 57 loop : -1.97 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 364 HIS 0.011 0.002 HIS B 18 PHE 0.032 0.003 PHE G 25 TYR 0.062 0.003 TYR B 88 ARG 0.014 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8541 (mttt) REVERT: K 369 PHE cc_start: 0.6774 (m-80) cc_final: 0.5935 (t80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3403 time to fit residues: 75.4719 Evaluate side-chains 138 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.0470 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN K 554 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17019 Z= 0.190 Angle : 0.583 8.620 24250 Z= 0.337 Chirality : 0.036 0.138 2753 Planarity : 0.004 0.054 2063 Dihedral : 28.788 157.922 4594 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.37 % Allowed : 3.89 % Favored : 95.74 % 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: 0.68 (0.25), residues: 1241 helix: 1.59 (0.19), residues: 775 sheet: -1.39 (0.71), residues: 57 loop : -1.53 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 206 HIS 0.003 0.001 HIS K 478 PHE 0.013 0.001 PHE K 274 TYR 0.026 0.001 TYR B 88 ARG 0.007 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 333 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8225 (mm-30) REVERT: K 369 PHE cc_start: 0.6440 (m-80) cc_final: 0.5694 (t80) REVERT: K 609 MET cc_start: 0.7780 (mpp) cc_final: 0.7449 (mpp) outliers start: 4 outliers final: 2 residues processed: 160 average time/residue: 0.3208 time to fit residues: 73.1294 Evaluate side-chains 143 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 68 ASN G 110 ASN K 143 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN K 554 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17019 Z= 0.227 Angle : 0.556 6.044 24250 Z= 0.325 Chirality : 0.036 0.136 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.708 157.602 4594 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.02 % Allowed : 5.37 % Favored : 93.61 % 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 (0.25), residues: 1241 helix: 1.72 (0.19), residues: 774 sheet: -1.16 (0.73), residues: 57 loop : -1.47 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 364 HIS 0.004 0.001 HIS K 478 PHE 0.015 0.001 PHE K 274 TYR 0.017 0.001 TYR F 51 ARG 0.006 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8597 (mtmt) REVERT: G 112 GLN cc_start: 0.8717 (mm110) cc_final: 0.8417 (mm110) REVERT: K 333 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8261 (mm-30) REVERT: K 369 PHE cc_start: 0.6666 (m-80) cc_final: 0.5640 (t80) outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 0.3230 time to fit residues: 70.1746 Evaluate side-chains 148 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 70 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 92 GLN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN K 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17019 Z= 0.210 Angle : 0.544 8.263 24250 Z= 0.318 Chirality : 0.035 0.133 2753 Planarity : 0.004 0.045 2063 Dihedral : 28.608 157.548 4594 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.83 % Allowed : 6.11 % Favored : 93.06 % 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: 0.94 (0.25), residues: 1241 helix: 1.76 (0.19), residues: 776 sheet: -1.08 (0.73), residues: 57 loop : -1.38 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.011 0.001 HIS K 402 PHE 0.013 0.001 PHE K 274 TYR 0.014 0.001 TYR F 51 ARG 0.005 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8615 (mtmt) REVERT: H 65 ASP cc_start: 0.8534 (t70) cc_final: 0.8277 (t0) REVERT: K 369 PHE cc_start: 0.6828 (m-80) cc_final: 0.5915 (t80) REVERT: K 388 GLU cc_start: 0.4704 (pt0) cc_final: 0.4367 (tp30) REVERT: K 609 MET cc_start: 0.7851 (mpp) cc_final: 0.7533 (mpp) outliers start: 9 outliers final: 8 residues processed: 158 average time/residue: 0.3236 time to fit residues: 73.3746 Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17019 Z= 0.286 Angle : 0.567 7.303 24250 Z= 0.330 Chirality : 0.037 0.130 2753 Planarity : 0.004 0.044 2063 Dihedral : 28.746 157.669 4594 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.93 % Allowed : 7.69 % Favored : 91.39 % 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: 0.96 (0.25), residues: 1241 helix: 1.75 (0.19), residues: 773 sheet: -1.08 (0.73), residues: 57 loop : -1.27 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.009 0.001 HIS K 402 PHE 0.015 0.002 PHE G 25 TYR 0.015 0.001 TYR F 51 ARG 0.005 0.000 ARG K 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8848 (m-10) cc_final: 0.8627 (m-80) REVERT: E 56 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8610 (mtmt) REVERT: H 65 ASP cc_start: 0.8581 (t70) cc_final: 0.8253 (t0) REVERT: K 369 PHE cc_start: 0.6920 (m-80) cc_final: 0.6019 (t80) REVERT: K 388 GLU cc_start: 0.4748 (pt0) cc_final: 0.4371 (tp30) outliers start: 10 outliers final: 6 residues processed: 153 average time/residue: 0.3110 time to fit residues: 68.4406 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17019 Z= 0.214 Angle : 0.559 11.433 24250 Z= 0.323 Chirality : 0.036 0.137 2753 Planarity : 0.004 0.052 2063 Dihedral : 28.706 157.483 4594 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.56 % Allowed : 8.80 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1241 helix: 1.82 (0.19), residues: 768 sheet: -1.05 (0.74), residues: 57 loop : -1.23 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 206 HIS 0.010 0.001 HIS K 402 PHE 0.010 0.001 PHE K 274 TYR 0.014 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8840 (m-10) cc_final: 0.8627 (m-80) REVERT: E 56 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8611 (mttt) REVERT: H 65 ASP cc_start: 0.8585 (t70) cc_final: 0.8265 (t0) REVERT: K 369 PHE cc_start: 0.6788 (m-80) cc_final: 0.6089 (t80) REVERT: K 388 GLU cc_start: 0.4716 (pt0) cc_final: 0.4365 (tp30) outliers start: 6 outliers final: 4 residues processed: 148 average time/residue: 0.3105 time to fit residues: 66.2025 Evaluate side-chains 142 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17019 Z= 0.280 Angle : 0.576 13.357 24250 Z= 0.330 Chirality : 0.037 0.131 2753 Planarity : 0.004 0.049 2063 Dihedral : 28.708 157.183 4594 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.65 % Allowed : 9.07 % Favored : 90.28 % 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 (0.25), residues: 1241 helix: 1.73 (0.19), residues: 771 sheet: -1.11 (0.72), residues: 57 loop : -1.32 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 206 HIS 0.008 0.001 HIS K 402 PHE 0.013 0.001 PHE G 25 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8864 (m-10) cc_final: 0.8628 (m-80) REVERT: H 65 ASP cc_start: 0.8601 (t70) cc_final: 0.8290 (t0) REVERT: K 333 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8133 (mm-30) REVERT: K 369 PHE cc_start: 0.7042 (m-80) cc_final: 0.6297 (t80) REVERT: K 388 GLU cc_start: 0.4700 (pt0) cc_final: 0.4273 (tp30) outliers start: 7 outliers final: 6 residues processed: 145 average time/residue: 0.3319 time to fit residues: 68.7645 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17019 Z= 0.301 Angle : 0.585 12.990 24250 Z= 0.335 Chirality : 0.037 0.166 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.757 157.243 4594 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.56 % Allowed : 9.54 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1241 helix: 1.66 (0.19), residues: 776 sheet: -1.10 (0.72), residues: 57 loop : -1.30 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 206 HIS 0.007 0.001 HIS K 402 PHE 0.014 0.002 PHE G 25 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8868 (m-10) cc_final: 0.8627 (m-80) REVERT: H 65 ASP cc_start: 0.8605 (t70) cc_final: 0.8295 (t0) REVERT: K 388 GLU cc_start: 0.4585 (pt0) cc_final: 0.4220 (tp30) outliers start: 6 outliers final: 6 residues processed: 142 average time/residue: 0.3305 time to fit residues: 67.2378 Evaluate side-chains 140 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN K 347 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17019 Z= 0.223 Angle : 0.571 11.880 24250 Z= 0.328 Chirality : 0.036 0.150 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.759 157.100 4594 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.74 % Allowed : 9.35 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1241 helix: 1.68 (0.19), residues: 777 sheet: -1.09 (0.72), residues: 57 loop : -1.26 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 206 HIS 0.008 0.001 HIS K 402 PHE 0.013 0.001 PHE K 369 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8846 (m-10) cc_final: 0.8615 (m-80) REVERT: G 35 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: H 65 ASP cc_start: 0.8595 (t70) cc_final: 0.8283 (t0) REVERT: K 388 GLU cc_start: 0.4579 (pt0) cc_final: 0.4218 (tp30) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.3262 time to fit residues: 67.7005 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 0.0020 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17019 Z= 0.254 Angle : 0.570 11.648 24250 Z= 0.328 Chirality : 0.036 0.152 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.681 157.141 4594 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.74 % Allowed : 9.35 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1241 helix: 1.68 (0.19), residues: 778 sheet: -1.14 (0.66), residues: 67 loop : -1.19 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 206 HIS 0.007 0.001 HIS K 402 PHE 0.011 0.001 PHE G 25 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8512 (tpp) cc_final: 0.8067 (tpp) REVERT: B 88 TYR cc_start: 0.8852 (m-10) cc_final: 0.8627 (m-80) REVERT: G 35 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7605 (ttp80) REVERT: H 65 ASP cc_start: 0.8597 (t70) cc_final: 0.8288 (t0) REVERT: K 388 GLU cc_start: 0.4625 (pt0) cc_final: 0.4186 (tp30) REVERT: K 476 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7766 (t) outliers start: 8 outliers final: 6 residues processed: 142 average time/residue: 0.3246 time to fit residues: 65.9526 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.092599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059185 restraints weight = 45896.223| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.00 r_work: 0.2818 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17019 Z= 0.199 Angle : 0.564 11.494 24250 Z= 0.325 Chirality : 0.035 0.148 2753 Planarity : 0.004 0.047 2063 Dihedral : 28.691 157.103 4594 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.83 % Allowed : 9.35 % Favored : 89.81 % 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: 0.98 (0.25), residues: 1241 helix: 1.71 (0.19), residues: 778 sheet: -1.14 (0.66), residues: 67 loop : -1.17 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 206 HIS 0.007 0.001 HIS K 402 PHE 0.009 0.001 PHE G 25 TYR 0.012 0.001 TYR F 51 ARG 0.004 0.000 ARG K 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.03 seconds wall clock time: 60 minutes 43.53 seconds (3643.53 seconds total)