Starting phenix.real_space_refine on Wed Feb 14 23:32:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5v_0682/02_2024/6j5v_0682_updated.pdb" } resolution = 4.25 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 6678 2.51 5 N 1810 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "A ASP 497": "OD1" <-> "OD2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B ARG 326": "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: 10529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6507 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 27, 'TRANS': 788} Chain breaks: 1 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1340 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 4 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL C 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL C 501 " occ=0.00 Time building chain proxies: 5.79, per 1000 atoms: 0.55 Number of scatterers: 10529 At special positions: 0 Unit cell: (87.28, 100.372, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 2 15.00 O 1976 8.00 N 1810 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL C 252 " - pdb=" N BQL C 501 " Simple link: pdb=" N LYS C 255 " - pdb=" C BQO C 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 1.9 seconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 34.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 4.550A pdb=" N GLU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 32 through 43 removed outlier: 5.403A pdb=" N GLU A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 56 through 59 No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 90 through 107 removed outlier: 3.896A pdb=" N HIS A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Proline residue: A 102 - end of helix Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 200 through 203 No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.263A pdb=" N TYR A 281 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 359 through 370 Processing helix chain 'A' and resid 376 through 390 removed outlier: 3.795A pdb=" N GLU A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.808A pdb=" N LEU A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 405 " --> pdb=" O MET A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.802A pdb=" N HIS A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 removed outlier: 4.139A pdb=" N ASP A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 removed outlier: 4.841A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 removed outlier: 3.654A pdb=" N THR A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 578 No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 679 through 682 removed outlier: 3.733A pdb=" N ASN A 682 " --> pdb=" O GLU A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 682' Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'C' and resid 194 through 209 removed outlier: 4.075A pdb=" N PHE C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.551A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 269' Processing helix chain 'C' and resid 275 through 291 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 361 through 364 No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'B' and resid 19 through 38 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 91 through 94 No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.533A pdb=" N ASN B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.218A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 removed outlier: 4.220A pdb=" N VAL B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.941A pdb=" N GLU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 4.252A pdb=" N LYS B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 removed outlier: 3.515A pdb=" N CYS B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 333 through 346 removed outlier: 4.356A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N SER B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 5.949A pdb=" N VAL A 563 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER A 537 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 565 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N CYS A 590 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 614 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL A 638 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 662 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS A 688 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A 715 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LEU A 691 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 717 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU A 743 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE A 718 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A 745 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 768 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU A 746 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 770 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A 795 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE A 771 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET A 797 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 820 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N LEU A 798 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 822 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.252A pdb=" N VAL B 136 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET B 85 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG B 76 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 65 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.906A pdb=" N ILE B 186 " --> pdb=" O LEU B 216 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1770 1.31 - 1.44: 2741 1.44 - 1.57: 6122 1.57 - 1.70: 5 1.70 - 1.82: 94 Bond restraints: 10732 Sorted by residual: bond pdb=" C2' BQO C 502 " pdb=" C3' BQO C 502 " ideal model delta sigma weight residual 1.635 1.465 0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C1' BQO C 502 " pdb=" C2' BQO C 502 " ideal model delta sigma weight residual 1.314 1.484 -0.170 2.00e-02 2.50e+03 7.18e+01 bond pdb=" C2 BQO C 502 " pdb=" N1 BQO C 502 " ideal model delta sigma weight residual 1.512 1.350 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" C3 BQO C 502 " pdb=" C3' BQO C 502 " ideal model delta sigma weight residual 1.322 1.482 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C4 BQO C 502 " pdb=" C5 BQO C 502 " ideal model delta sigma weight residual 1.508 1.358 0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 10727 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.90: 207 105.90 - 113.29: 5884 113.29 - 120.69: 4835 120.69 - 128.08: 3469 128.08 - 135.48: 106 Bond angle restraints: 14501 Sorted by residual: angle pdb=" N CYS A 649 " pdb=" CA CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sigma weight residual 114.17 108.33 5.84 1.14e+00 7.69e-01 2.63e+01 angle pdb=" CA LEU A 612 " pdb=" CB LEU A 612 " pdb=" CG LEU A 612 " ideal model delta sigma weight residual 116.30 133.09 -16.79 3.50e+00 8.16e-02 2.30e+01 angle pdb=" CA THR A 541 " pdb=" CB THR A 541 " pdb=" CG2 THR A 541 " ideal model delta sigma weight residual 110.50 118.44 -7.94 1.70e+00 3.46e-01 2.18e+01 angle pdb=" C ASN A 611 " pdb=" N LEU A 612 " pdb=" CA LEU A 612 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C GLU B 80 " pdb=" N ASP B 81 " pdb=" CA ASP B 81 " ideal model delta sigma weight residual 122.61 129.34 -6.73 1.56e+00 4.11e-01 1.86e+01 ... (remaining 14496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5586 17.65 - 35.30: 758 35.30 - 52.95: 154 52.95 - 70.60: 18 70.60 - 88.25: 9 Dihedral angle restraints: 6525 sinusoidal: 2708 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 141.18 38.82 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA CYS A 649 " pdb=" C CYS A 649 " pdb=" N PHE A 650 " pdb=" CA PHE A 650 " ideal model delta harmonic sigma weight residual 180.00 143.13 36.87 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLU A 648 " pdb=" C GLU A 648 " pdb=" N CYS A 649 " pdb=" CA CYS A 649 " ideal model delta harmonic sigma weight residual 180.00 145.49 34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 6522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1096 0.057 - 0.114: 393 0.114 - 0.171: 113 0.171 - 0.227: 27 0.227 - 0.284: 5 Chirality restraints: 1634 Sorted by residual: chirality pdb=" CB VAL B 251 " pdb=" CA VAL B 251 " pdb=" CG1 VAL B 251 " pdb=" CG2 VAL B 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA THR A 541 " pdb=" N THR A 541 " pdb=" C THR A 541 " pdb=" CB THR A 541 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU A 818 " pdb=" CB LEU A 818 " pdb=" CD1 LEU A 818 " pdb=" CD2 LEU A 818 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1631 not shown) Planarity restraints: 1840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 44 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 781 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 782 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 782 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 782 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 312 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 313 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 313 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 313 " -0.040 5.00e-02 4.00e+02 ... (remaining 1837 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2732 2.79 - 3.32: 10323 3.32 - 3.85: 18313 3.85 - 4.37: 20284 4.37 - 4.90: 32299 Nonbonded interactions: 83951 Sorted by model distance: nonbonded pdb=" O GLN A 621 " pdb=" OG SER A 646 " model vdw 2.263 2.440 nonbonded pdb=" O GLY A 785 " pdb=" OG1 THR A 789 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR A 749 " pdb=" O SER A 753 " model vdw 2.314 2.440 nonbonded pdb=" OG SER A 576 " pdb=" O GLN A 601 " model vdw 2.316 2.440 nonbonded pdb=" O LEU C 205 " pdb=" ND1 HIS C 209 " model vdw 2.325 2.520 ... (remaining 83946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.470 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.720 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.008 0.170 10732 Z= 0.552 Angle : 1.194 16.788 14501 Z= 0.631 Chirality : 0.066 0.284 1634 Planarity : 0.008 0.102 1838 Dihedral : 16.372 88.247 4047 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 0.94 % Allowed : 15.83 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.32 % 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: -4.88 (0.19), residues: 1297 helix: -3.12 (0.16), residues: 469 sheet: -2.90 (0.48), residues: 89 loop : -3.50 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 844 HIS 0.010 0.002 HIS B 196 PHE 0.023 0.003 PHE B 244 TYR 0.042 0.003 TYR A 721 ARG 0.012 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 MET cc_start: 0.8911 (tpp) cc_final: 0.8705 (tpp) REVERT: A 714 MET cc_start: 0.8312 (tpp) cc_final: 0.7819 (mmm) REVERT: A 829 LEU cc_start: 0.9030 (mt) cc_final: 0.8555 (mt) REVERT: C 217 TYR cc_start: 0.7998 (t80) cc_final: 0.7190 (t80) REVERT: C 219 ASP cc_start: 0.8089 (m-30) cc_final: 0.7830 (m-30) REVERT: C 224 ASN cc_start: 0.8904 (m-40) cc_final: 0.8609 (t0) REVERT: C 231 PHE cc_start: 0.8522 (m-80) cc_final: 0.8268 (m-10) REVERT: C 293 ARG cc_start: 0.6152 (mpp-170) cc_final: 0.5542 (mtm-85) REVERT: C 294 ARG cc_start: 0.8273 (ptp90) cc_final: 0.7961 (ptm160) REVERT: C 359 MET cc_start: 0.7366 (tpp) cc_final: 0.6925 (tmm) REVERT: B 68 GLN cc_start: 0.8918 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 138 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 171 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8479 (mm-30) REVERT: B 244 PHE cc_start: 0.8224 (p90) cc_final: 0.7633 (p90) REVERT: B 247 GLU cc_start: 0.8711 (tp30) cc_final: 0.8346 (tp30) REVERT: B 313 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 335 GLN cc_start: 0.9226 (mp10) cc_final: 0.8973 (mp10) outliers start: 11 outliers final: 5 residues processed: 237 average time/residue: 0.2451 time to fit residues: 79.5138 Evaluate side-chains 171 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 178 ASN A 204 ASN A 273 ASN A 335 ASN A 377 HIS A 393 ASN A 435 GLN A 467 ASN A 520 ASN A 611 ASN A 621 GLN A 673 ASN A 742 HIS A 788 ASN A 812 GLN C 298 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 311 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10732 Z= 0.178 Angle : 0.727 14.811 14501 Z= 0.360 Chirality : 0.046 0.193 1634 Planarity : 0.005 0.087 1838 Dihedral : 7.912 66.710 1457 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.89 (0.21), residues: 1297 helix: -1.74 (0.22), residues: 456 sheet: -3.34 (0.44), residues: 103 loop : -3.15 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 757 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE B 244 TYR 0.028 0.001 TYR B 252 ARG 0.005 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8528 (mtpt) REVERT: A 428 ASP cc_start: 0.8711 (t0) cc_final: 0.8489 (p0) REVERT: A 469 CYS cc_start: 0.8477 (t) cc_final: 0.8244 (t) REVERT: A 599 LEU cc_start: 0.9282 (tp) cc_final: 0.9063 (tp) REVERT: A 604 ARG cc_start: 0.8888 (tmt-80) cc_final: 0.8402 (tpt90) REVERT: C 217 TYR cc_start: 0.7749 (t80) cc_final: 0.7452 (t80) REVERT: C 219 ASP cc_start: 0.7757 (m-30) cc_final: 0.7447 (m-30) REVERT: C 272 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7933 (mmm-85) REVERT: C 294 ARG cc_start: 0.8318 (ptp90) cc_final: 0.7947 (ptm160) REVERT: C 296 MET cc_start: 0.6406 (tmm) cc_final: 0.6197 (tmm) REVERT: C 325 MET cc_start: 0.8149 (ppp) cc_final: 0.7438 (ppp) REVERT: C 356 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8321 (ttm170) REVERT: C 361 GLU cc_start: 0.8907 (pt0) cc_final: 0.8510 (pp20) REVERT: B 68 GLN cc_start: 0.8976 (tt0) cc_final: 0.8716 (tm-30) REVERT: B 103 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 121 LEU cc_start: 0.9256 (tp) cc_final: 0.9028 (tp) REVERT: B 138 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 199 LEU cc_start: 0.8687 (tt) cc_final: 0.8373 (mt) REVERT: B 313 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8279 (tm-30) outliers start: 3 outliers final: 1 residues processed: 222 average time/residue: 0.2268 time to fit residues: 71.0949 Evaluate side-chains 164 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10732 Z= 0.181 Angle : 0.715 13.806 14501 Z= 0.353 Chirality : 0.046 0.174 1634 Planarity : 0.005 0.086 1838 Dihedral : 7.372 63.809 1457 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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: -3.32 (0.22), residues: 1297 helix: -1.21 (0.23), residues: 454 sheet: -2.73 (0.47), residues: 99 loop : -2.90 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 757 HIS 0.010 0.001 HIS C 209 PHE 0.017 0.002 PHE C 207 TYR 0.017 0.002 TYR A 109 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 SER cc_start: 0.8323 (p) cc_final: 0.8122 (p) REVERT: A 428 ASP cc_start: 0.8752 (t0) cc_final: 0.8474 (p0) REVERT: A 469 CYS cc_start: 0.8479 (t) cc_final: 0.8244 (t) REVERT: A 604 ARG cc_start: 0.8790 (tmt-80) cc_final: 0.8451 (tpt90) REVERT: A 639 LEU cc_start: 0.9111 (tp) cc_final: 0.8864 (tp) REVERT: A 648 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7468 (tp30) REVERT: A 731 LYS cc_start: 0.8430 (pttm) cc_final: 0.7980 (pttp) REVERT: A 741 LEU cc_start: 0.9154 (tp) cc_final: 0.8923 (tp) REVERT: A 826 CYS cc_start: 0.7846 (p) cc_final: 0.7421 (p) REVERT: A 829 LEU cc_start: 0.9201 (mt) cc_final: 0.8191 (mt) REVERT: C 184 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8520 (mmm160) REVERT: C 208 LEU cc_start: 0.8881 (mt) cc_final: 0.8670 (mt) REVERT: C 219 ASP cc_start: 0.7672 (m-30) cc_final: 0.7379 (m-30) REVERT: C 224 ASN cc_start: 0.8616 (m-40) cc_final: 0.8214 (m-40) REVERT: C 294 ARG cc_start: 0.8260 (ptp90) cc_final: 0.7911 (ptm160) REVERT: C 361 GLU cc_start: 0.9015 (pt0) cc_final: 0.8568 (pp20) REVERT: B 71 TYR cc_start: 0.7833 (m-80) cc_final: 0.7531 (m-80) REVERT: B 121 LEU cc_start: 0.9284 (tp) cc_final: 0.8993 (tp) REVERT: B 138 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 199 LEU cc_start: 0.8641 (tt) cc_final: 0.8412 (mt) REVERT: B 222 ARG cc_start: 0.8544 (ttt-90) cc_final: 0.8166 (tpt-90) REVERT: B 313 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2355 time to fit residues: 68.4140 Evaluate side-chains 165 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 0.0040 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10732 Z= 0.221 Angle : 0.733 15.834 14501 Z= 0.361 Chirality : 0.047 0.176 1634 Planarity : 0.005 0.083 1838 Dihedral : 7.289 62.506 1457 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.30 (0.22), residues: 1297 helix: -1.16 (0.23), residues: 484 sheet: -2.77 (0.48), residues: 95 loop : -2.97 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 757 HIS 0.008 0.001 HIS C 209 PHE 0.019 0.002 PHE C 207 TYR 0.015 0.002 TYR B 252 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.8595 (mmp) cc_final: 0.8057 (mmp) REVERT: A 413 SER cc_start: 0.8355 (p) cc_final: 0.8118 (p) REVERT: A 604 ARG cc_start: 0.8842 (tmt-80) cc_final: 0.8241 (tpt90) REVERT: A 688 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8863 (mttt) REVERT: A 731 LYS cc_start: 0.8513 (pttm) cc_final: 0.8085 (pttp) REVERT: A 741 LEU cc_start: 0.9125 (tp) cc_final: 0.8878 (tp) REVERT: A 828 GLU cc_start: 0.8658 (tp30) cc_final: 0.8070 (tp30) REVERT: C 184 ARG cc_start: 0.8931 (mmm160) cc_final: 0.8692 (mmm160) REVERT: C 217 TYR cc_start: 0.7577 (t80) cc_final: 0.7309 (t80) REVERT: C 272 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: C 282 PHE cc_start: 0.8843 (t80) cc_final: 0.8597 (t80) REVERT: C 293 ARG cc_start: 0.7203 (mpp80) cc_final: 0.6712 (mtm-85) REVERT: C 294 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7874 (ptm160) REVERT: C 296 MET cc_start: 0.6908 (tmm) cc_final: 0.6619 (tmm) REVERT: C 361 GLU cc_start: 0.8940 (pt0) cc_final: 0.8509 (pp20) REVERT: B 71 TYR cc_start: 0.8075 (m-80) cc_final: 0.7828 (m-80) REVERT: B 121 LEU cc_start: 0.9306 (tp) cc_final: 0.8985 (tp) REVERT: B 138 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 235 ILE cc_start: 0.8047 (mm) cc_final: 0.7847 (mm) REVERT: B 313 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8357 (tm-30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2272 time to fit residues: 65.7155 Evaluate side-chains 162 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 90 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN A 587 HIS A 627 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10732 Z= 0.258 Angle : 0.751 16.582 14501 Z= 0.371 Chirality : 0.047 0.196 1634 Planarity : 0.005 0.084 1838 Dihedral : 7.309 62.989 1457 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.23 (0.22), residues: 1297 helix: -1.03 (0.23), residues: 478 sheet: -2.95 (0.44), residues: 99 loop : -2.92 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 757 HIS 0.006 0.002 HIS A 377 PHE 0.024 0.002 PHE A 748 TYR 0.035 0.002 TYR A 721 ARG 0.006 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.9076 (mmt) cc_final: 0.8633 (mmm) REVERT: A 828 GLU cc_start: 0.8632 (tp30) cc_final: 0.8186 (tp30) REVERT: C 184 ARG cc_start: 0.8936 (mmm160) cc_final: 0.8675 (mmm160) REVERT: C 217 TYR cc_start: 0.7641 (t80) cc_final: 0.7153 (t80) REVERT: C 282 PHE cc_start: 0.8815 (t80) cc_final: 0.8578 (t80) REVERT: C 294 ARG cc_start: 0.8304 (ptp90) cc_final: 0.8095 (ptp90) REVERT: C 356 ARG cc_start: 0.8883 (ttm170) cc_final: 0.8316 (ttm170) REVERT: C 359 MET cc_start: 0.6371 (tpt) cc_final: 0.5907 (tpt) REVERT: C 361 GLU cc_start: 0.8838 (pt0) cc_final: 0.8472 (pp20) REVERT: B 121 LEU cc_start: 0.9290 (tp) cc_final: 0.8943 (tp) REVERT: B 138 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2346 time to fit residues: 67.6178 Evaluate side-chains 151 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 434 GLN A 627 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10732 Z= 0.201 Angle : 0.750 15.583 14501 Z= 0.363 Chirality : 0.046 0.191 1634 Planarity : 0.005 0.083 1838 Dihedral : 7.121 60.973 1457 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -3.09 (0.22), residues: 1297 helix: -0.97 (0.23), residues: 470 sheet: -2.44 (0.56), residues: 77 loop : -2.88 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 173 HIS 0.009 0.001 HIS C 209 PHE 0.021 0.002 PHE A 783 TYR 0.015 0.001 TYR B 71 ARG 0.007 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.9065 (mmt) cc_final: 0.8714 (mmm) REVERT: A 109 TYR cc_start: 0.8570 (p90) cc_final: 0.8335 (p90) REVERT: A 266 MET cc_start: 0.8660 (mmp) cc_final: 0.8212 (mmp) REVERT: A 368 LEU cc_start: 0.9248 (tp) cc_final: 0.8930 (tp) REVERT: A 413 SER cc_start: 0.8207 (p) cc_final: 0.7960 (p) REVERT: A 459 GLU cc_start: 0.8297 (mp0) cc_final: 0.7885 (mp0) REVERT: A 828 GLU cc_start: 0.8615 (tp30) cc_final: 0.8133 (tp30) REVERT: C 184 ARG cc_start: 0.8951 (mmm160) cc_final: 0.8729 (mmm160) REVERT: C 217 TYR cc_start: 0.7809 (t80) cc_final: 0.7378 (t80) REVERT: C 219 ASP cc_start: 0.7594 (m-30) cc_final: 0.7373 (m-30) REVERT: C 272 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: C 282 PHE cc_start: 0.8769 (t80) cc_final: 0.8523 (t80) REVERT: C 294 ARG cc_start: 0.8245 (ptp90) cc_final: 0.8011 (ptp90) REVERT: C 359 MET cc_start: 0.6501 (tpt) cc_final: 0.6049 (tpt) REVERT: C 361 GLU cc_start: 0.8835 (pt0) cc_final: 0.8478 (pp20) REVERT: B 121 LEU cc_start: 0.9294 (tp) cc_final: 0.8908 (tp) REVERT: B 138 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 235 ILE cc_start: 0.8076 (mm) cc_final: 0.7759 (mm) REVERT: B 313 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8276 (tm-30) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2309 time to fit residues: 66.0116 Evaluate side-chains 160 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.163 Angle : 0.753 14.483 14501 Z= 0.357 Chirality : 0.047 0.190 1634 Planarity : 0.005 0.081 1838 Dihedral : 6.899 57.059 1457 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -2.93 (0.23), residues: 1297 helix: -0.94 (0.23), residues: 473 sheet: -2.23 (0.54), residues: 87 loop : -2.70 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 757 HIS 0.007 0.001 HIS C 209 PHE 0.017 0.002 PHE A 386 TYR 0.014 0.001 TYR B 105 ARG 0.007 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.8489 (m-30) cc_final: 0.7556 (p0) REVERT: A 41 MET cc_start: 0.9034 (mmt) cc_final: 0.8581 (mmm) REVERT: A 109 TYR cc_start: 0.8502 (p90) cc_final: 0.8215 (p90) REVERT: A 413 SER cc_start: 0.7962 (p) cc_final: 0.7494 (p) REVERT: A 428 ASP cc_start: 0.8784 (t0) cc_final: 0.8519 (p0) REVERT: A 469 CYS cc_start: 0.8408 (t) cc_final: 0.8186 (t) REVERT: A 599 LEU cc_start: 0.9260 (tp) cc_final: 0.9058 (tp) REVERT: A 828 GLU cc_start: 0.8636 (tp30) cc_final: 0.8205 (tm-30) REVERT: C 217 TYR cc_start: 0.7717 (t80) cc_final: 0.7390 (t80) REVERT: C 219 ASP cc_start: 0.7565 (m-30) cc_final: 0.7363 (m-30) REVERT: C 272 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7508 (mmm-85) REVERT: C 294 ARG cc_start: 0.8318 (ptp90) cc_final: 0.7846 (ptm160) REVERT: C 359 MET cc_start: 0.6474 (tpt) cc_final: 0.6016 (tpt) REVERT: C 361 GLU cc_start: 0.8821 (pt0) cc_final: 0.8504 (pp20) REVERT: B 52 GLN cc_start: 0.8953 (mt0) cc_final: 0.8749 (mt0) REVERT: B 71 TYR cc_start: 0.7868 (m-80) cc_final: 0.7667 (m-10) REVERT: B 121 LEU cc_start: 0.9305 (tp) cc_final: 0.8928 (tp) REVERT: B 137 PHE cc_start: 0.8948 (m-80) cc_final: 0.8634 (m-80) REVERT: B 138 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 199 LEU cc_start: 0.8778 (tp) cc_final: 0.8571 (tp) REVERT: B 313 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8231 (tm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2263 time to fit residues: 69.4646 Evaluate side-chains 169 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 747 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10732 Z= 0.191 Angle : 0.744 15.158 14501 Z= 0.356 Chirality : 0.046 0.176 1634 Planarity : 0.005 0.081 1838 Dihedral : 6.844 56.383 1457 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.88 (0.22), residues: 1297 helix: -0.81 (0.23), residues: 466 sheet: -2.11 (0.59), residues: 73 loop : -2.75 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 757 HIS 0.006 0.001 HIS A 377 PHE 0.021 0.002 PHE A 633 TYR 0.011 0.001 TYR B 178 ARG 0.011 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.8482 (p90) cc_final: 0.8209 (p90) REVERT: A 187 PHE cc_start: 0.6382 (m-80) cc_final: 0.6117 (m-80) REVERT: A 368 LEU cc_start: 0.9267 (tp) cc_final: 0.8962 (tp) REVERT: A 413 SER cc_start: 0.8096 (p) cc_final: 0.7848 (p) REVERT: A 828 GLU cc_start: 0.8670 (tp30) cc_final: 0.8293 (tm-30) REVERT: C 217 TYR cc_start: 0.7762 (t80) cc_final: 0.7409 (t80) REVERT: C 219 ASP cc_start: 0.7502 (m-30) cc_final: 0.7248 (m-30) REVERT: C 272 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: C 294 ARG cc_start: 0.8185 (ptp90) cc_final: 0.7930 (ptp90) REVERT: C 356 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8339 (ttm170) REVERT: C 359 MET cc_start: 0.6326 (tpt) cc_final: 0.5825 (tpt) REVERT: C 361 GLU cc_start: 0.8850 (pt0) cc_final: 0.8552 (pp20) REVERT: B 121 LEU cc_start: 0.9350 (tp) cc_final: 0.8947 (tp) REVERT: B 137 PHE cc_start: 0.8987 (m-80) cc_final: 0.8698 (m-80) REVERT: B 138 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 251 VAL cc_start: 0.9584 (m) cc_final: 0.9240 (m) REVERT: B 313 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8283 (tm-30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2037 time to fit residues: 61.8729 Evaluate side-chains 159 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.0270 overall best weight: 1.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 747 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.170 Angle : 0.746 14.586 14501 Z= 0.354 Chirality : 0.047 0.186 1634 Planarity : 0.005 0.080 1838 Dihedral : 6.741 53.900 1457 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.80 (0.22), residues: 1297 helix: -0.77 (0.24), residues: 450 sheet: -2.17 (0.56), residues: 83 loop : -2.63 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 173 HIS 0.006 0.001 HIS A 377 PHE 0.020 0.002 PHE A 633 TYR 0.012 0.001 TYR B 105 ARG 0.006 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.8430 (m-30) cc_final: 0.7520 (p0) REVERT: A 109 TYR cc_start: 0.8506 (p90) cc_final: 0.8252 (p90) REVERT: A 187 PHE cc_start: 0.6548 (m-80) cc_final: 0.6100 (m-80) REVERT: A 368 LEU cc_start: 0.9252 (tp) cc_final: 0.8957 (tp) REVERT: A 413 SER cc_start: 0.7922 (p) cc_final: 0.7453 (p) REVERT: A 459 GLU cc_start: 0.8398 (mp0) cc_final: 0.8075 (mp0) REVERT: A 815 MET cc_start: 0.9190 (mmm) cc_final: 0.8981 (mmm) REVERT: A 828 GLU cc_start: 0.8613 (tp30) cc_final: 0.8349 (tm-30) REVERT: C 217 TYR cc_start: 0.7693 (t80) cc_final: 0.7413 (t80) REVERT: C 219 ASP cc_start: 0.7484 (m-30) cc_final: 0.7209 (m-30) REVERT: C 272 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7485 (mmm-85) REVERT: C 294 ARG cc_start: 0.8266 (ptp90) cc_final: 0.8018 (ptp90) REVERT: C 356 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8213 (ttm170) REVERT: C 359 MET cc_start: 0.6300 (tpt) cc_final: 0.5792 (tpt) REVERT: C 361 GLU cc_start: 0.8854 (pt0) cc_final: 0.8559 (pp20) REVERT: B 52 GLN cc_start: 0.8996 (mt0) cc_final: 0.8749 (mt0) REVERT: B 71 TYR cc_start: 0.7590 (m-10) cc_final: 0.7319 (m-10) REVERT: B 121 LEU cc_start: 0.9362 (tp) cc_final: 0.9001 (tp) REVERT: B 122 GLN cc_start: 0.8679 (mt0) cc_final: 0.8385 (mt0) REVERT: B 137 PHE cc_start: 0.8983 (m-80) cc_final: 0.8659 (m-80) REVERT: B 138 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 251 VAL cc_start: 0.9514 (m) cc_final: 0.9312 (m) REVERT: B 313 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8315 (tm-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2098 time to fit residues: 63.9306 Evaluate side-chains 169 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN C 187 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.180 Angle : 0.755 14.845 14501 Z= 0.357 Chirality : 0.046 0.187 1634 Planarity : 0.005 0.080 1838 Dihedral : 6.742 54.066 1457 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.75 (0.23), residues: 1297 helix: -0.72 (0.24), residues: 449 sheet: -2.18 (0.56), residues: 85 loop : -2.60 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 173 HIS 0.006 0.001 HIS A 377 PHE 0.019 0.002 PHE A 633 TYR 0.011 0.001 TYR B 105 ARG 0.007 0.000 ARG B 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.8375 (m-30) cc_final: 0.7423 (p0) REVERT: A 41 MET cc_start: 0.9048 (mmt) cc_final: 0.8602 (mmm) REVERT: A 109 TYR cc_start: 0.8584 (p90) cc_final: 0.8358 (p90) REVERT: A 187 PHE cc_start: 0.6609 (m-80) cc_final: 0.6070 (m-80) REVERT: A 413 SER cc_start: 0.7884 (p) cc_final: 0.7466 (p) REVERT: A 459 GLU cc_start: 0.8430 (mp0) cc_final: 0.8071 (mp0) REVERT: C 217 TYR cc_start: 0.7545 (t80) cc_final: 0.7137 (t80) REVERT: C 219 ASP cc_start: 0.7377 (m-30) cc_final: 0.6863 (m-30) REVERT: C 220 PHE cc_start: 0.7360 (t80) cc_final: 0.7040 (t80) REVERT: C 272 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7485 (mmm-85) REVERT: C 282 PHE cc_start: 0.8869 (t80) cc_final: 0.8667 (t80) REVERT: C 294 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7940 (ptp90) REVERT: C 356 ARG cc_start: 0.8453 (mtm180) cc_final: 0.8174 (ttm170) REVERT: C 359 MET cc_start: 0.6188 (tpt) cc_final: 0.5666 (tpt) REVERT: C 361 GLU cc_start: 0.8872 (pt0) cc_final: 0.8592 (pp20) REVERT: B 52 GLN cc_start: 0.9002 (mt0) cc_final: 0.8743 (mt0) REVERT: B 121 LEU cc_start: 0.9353 (tp) cc_final: 0.9004 (tp) REVERT: B 122 GLN cc_start: 0.8670 (mt0) cc_final: 0.8273 (tt0) REVERT: B 137 PHE cc_start: 0.8993 (m-80) cc_final: 0.8698 (m-80) REVERT: B 138 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 313 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8324 (tm-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2159 time to fit residues: 65.8881 Evaluate side-chains 162 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN C 335 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092475 restraints weight = 28902.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095099 restraints weight = 16966.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096829 restraints weight = 11626.498| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.163 Angle : 0.752 14.436 14501 Z= 0.355 Chirality : 0.046 0.171 1634 Planarity : 0.005 0.080 1838 Dihedral : 6.589 59.622 1457 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.72 (0.23), residues: 1297 helix: -0.79 (0.24), residues: 448 sheet: -2.04 (0.57), residues: 83 loop : -2.53 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 173 HIS 0.007 0.001 HIS A 377 PHE 0.018 0.001 PHE A 633 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG C 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.88 seconds wall clock time: 43 minutes 0.05 seconds (2580.05 seconds total)