Starting phenix.real_space_refine on Wed Feb 14 05:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wix_32539/02_2024/7wix_32539_updated.pdb" } resolution = 3.53 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 5521 2.51 5 N 1557 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" 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: 8670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.03, per 1000 atoms: 0.58 Number of scatterers: 8670 At special positions: 0 Unit cell: (69.7, 98.4, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 4 15.00 Mg 1 11.99 O 1573 8.00 N 1557 7.00 C 5521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 3 sheets defined 60.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.745A pdb=" N LEU A 289 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Proline residue: A 292 - end of helix removed outlier: 3.680A pdb=" N ALA A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 327 through 374 Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.519A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 429 removed outlier: 4.875A pdb=" N VAL A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Proline residue: A 410 - end of helix Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 454 removed outlier: 3.911A pdb=" N LEU A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 456 through 478 removed outlier: 3.986A pdb=" N VAL A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 510 through 522 removed outlier: 4.201A pdb=" N GLY A 513 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 514 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 520 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 521 " --> pdb=" O MET A 518 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 540 Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.864A pdb=" N LEU A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Proline residue: A 551 - end of helix removed outlier: 3.841A pdb=" N LEU A 555 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 572 removed outlier: 3.636A pdb=" N LEU A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.705A pdb=" N TYR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 683' Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 782 through 791 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'B' and resid 14 through 44 removed outlier: 4.231A pdb=" N THR B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 50 through 95 removed outlier: 3.769A pdb=" N ALA B 53 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 55 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 94 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 121 through 149 removed outlier: 4.568A pdb=" N VAL B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Proline residue: B 134 - end of helix Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 154 through 201 removed outlier: 4.264A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 4.854A pdb=" N ARG B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 232 through 264 Proline residue: B 239 - end of helix removed outlier: 4.087A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 311 Proline residue: B 286 - end of helix removed outlier: 3.920A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 3.707A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 402 through 405 No H-bonds generated for 'chain 'B' and resid 402 through 405' Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 449 through 452 No H-bonds generated for 'chain 'B' and resid 449 through 452' Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.883A pdb=" N ARG B 477 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 484 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 528 through 533 removed outlier: 4.108A pdb=" N HIS B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 Processing helix chain 'B' and resid 561 through 571 Processing sheet with id= A, first strand: chain 'A' and resid 821 through 825 removed outlier: 3.544A pdb=" N VAL A 822 " --> pdb=" O VAL A 815 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 815 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG A 824 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 813 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 332 through 335 removed outlier: 4.038A pdb=" N GLU B 333 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP B 335 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 389 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.536A pdb=" N ILE B 523 " --> pdb=" O THR B 362 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1128 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: 2.31 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1407 1.31 - 1.43: 2266 1.43 - 1.56: 5134 1.56 - 1.68: 6 1.68 - 1.81: 23 Bond restraints: 8836 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C VAL A 611 " pdb=" O VAL A 611 " ideal model delta sigma weight residual 1.236 1.186 0.050 9.90e-03 1.02e+04 2.59e+01 bond pdb=" C5 ADP A 901 " pdb=" C6 ADP A 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C5 ADP B 601 " pdb=" C6 ADP B 601 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.80: 161 104.80 - 112.10: 4653 112.10 - 119.39: 2750 119.39 - 126.69: 4362 126.69 - 133.98: 155 Bond angle restraints: 12081 Sorted by residual: angle pdb=" N PRO A 607 " pdb=" CA PRO A 607 " pdb=" C PRO A 607 " ideal model delta sigma weight residual 112.47 101.44 11.03 2.06e+00 2.36e-01 2.87e+01 angle pdb=" O ALA B 229 " pdb=" C ALA B 229 " pdb=" N THR B 230 " ideal model delta sigma weight residual 121.47 125.36 -3.89 7.50e-01 1.78e+00 2.69e+01 angle pdb=" C ALA B 229 " pdb=" CA ALA B 229 " pdb=" CB ALA B 229 " ideal model delta sigma weight residual 117.07 110.29 6.78 1.44e+00 4.82e-01 2.22e+01 angle pdb=" CA ALA B 229 " pdb=" C ALA B 229 " pdb=" N THR B 230 " ideal model delta sigma weight residual 120.47 115.63 4.84 1.03e+00 9.43e-01 2.21e+01 angle pdb=" N THR A 522 " pdb=" CA THR A 522 " pdb=" C THR A 522 " ideal model delta sigma weight residual 114.75 108.95 5.80 1.26e+00 6.30e-01 2.12e+01 ... (remaining 12076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.86: 5033 28.86 - 57.73: 166 57.73 - 86.59: 20 86.59 - 115.46: 1 115.46 - 144.32: 3 Dihedral angle restraints: 5223 sinusoidal: 1962 harmonic: 3261 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 84.32 -144.32 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 69.06 -129.06 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 66.48 -126.48 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1306 0.068 - 0.136: 148 0.136 - 0.203: 12 0.203 - 0.271: 2 0.271 - 0.339: 2 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA HIS B 227 " pdb=" N HIS B 227 " pdb=" C HIS B 227 " pdb=" CB HIS B 227 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA THR B 230 " pdb=" N THR B 230 " pdb=" C THR B 230 " pdb=" CB THR B 230 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB THR B 230 " pdb=" CA THR B 230 " pdb=" OG1 THR B 230 " pdb=" CG2 THR B 230 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1467 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 97 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO B 98 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 605 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLU A 605 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU A 605 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 606 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 836 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ARG A 836 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG A 836 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 837 " -0.018 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 111 2.63 - 3.20: 8426 3.20 - 3.77: 13389 3.77 - 4.33: 16981 4.33 - 4.90: 28750 Nonbonded interactions: 67657 Sorted by model distance: nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 2.063 2.170 nonbonded pdb=" OE2 GLU A 681 " pdb=" NH2 ARG A 685 " model vdw 2.237 2.520 nonbonded pdb=" O GLU A 605 " pdb=" CG2 THR A 609 " model vdw 2.261 3.460 nonbonded pdb=" O GLU B 465 " pdb=" OG SER B 468 " model vdw 2.264 2.440 nonbonded pdb=" O ASP A 680 " pdb=" OG1 THR A 684 " model vdw 2.279 2.440 ... (remaining 67652 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=1.00 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: 3.640 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: 11.990 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.430 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 8836 Z= 0.329 Angle : 0.925 12.123 12081 Z= 0.550 Chirality : 0.045 0.339 1470 Planarity : 0.005 0.100 1538 Dihedral : 14.856 144.323 3121 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.15 % Favored : 89.50 % Rotamer: Outliers : 0.57 % Allowed : 6.70 % Favored : 92.73 % Cbeta Deviations : 0.10 % 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: -2.81 (0.22), residues: 1143 helix: -0.61 (0.18), residues: 711 sheet: -2.68 (0.61), residues: 62 loop : -4.20 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.010 0.001 HIS B 227 PHE 0.024 0.001 PHE B 334 TYR 0.008 0.001 TYR A 736 ARG 0.003 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.956 Fit side-chains REVERT: A 691 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6798 (mm-40) outliers start: 5 outliers final: 5 residues processed: 103 average time/residue: 0.2501 time to fit residues: 34.1106 Evaluate side-chains 62 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 582 HIS A 703 ASN A 752 GLN B 204 GLN B 420 HIS B 438 GLN B 504 ASN B 569 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8836 Z= 0.220 Angle : 0.697 8.431 12081 Z= 0.348 Chirality : 0.042 0.151 1470 Planarity : 0.006 0.096 1538 Dihedral : 9.040 135.955 1279 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.19 % Favored : 90.64 % Rotamer: Outliers : 3.07 % Allowed : 13.75 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -1.51 (0.25), residues: 1143 helix: 0.42 (0.20), residues: 716 sheet: -2.21 (0.62), residues: 64 loop : -3.76 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 56 HIS 0.004 0.001 HIS A 597 PHE 0.025 0.001 PHE B 334 TYR 0.011 0.001 TYR A 444 ARG 0.003 0.000 ARG A 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8964 (tmtt) REVERT: B 231 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7533 (mmm) REVERT: B 236 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7491 (mmt) outliers start: 27 outliers final: 13 residues processed: 91 average time/residue: 0.2675 time to fit residues: 35.9729 Evaluate side-chains 79 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8836 Z= 0.164 Angle : 0.646 8.391 12081 Z= 0.319 Chirality : 0.040 0.150 1470 Planarity : 0.005 0.090 1538 Dihedral : 8.505 136.677 1277 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.84 % Favored : 90.99 % Rotamer: Outliers : 3.86 % Allowed : 15.68 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -1.02 (0.25), residues: 1143 helix: 0.76 (0.20), residues: 712 sheet: -2.04 (0.58), residues: 79 loop : -3.44 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.002 0.001 HIS A 597 PHE 0.019 0.001 PHE B 334 TYR 0.006 0.001 TYR A 425 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8880 (tmtt) REVERT: A 397 ASP cc_start: 0.8506 (m-30) cc_final: 0.8299 (m-30) REVERT: A 454 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8437 (tm-30) REVERT: B 120 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8854 (m) REVERT: B 231 MET cc_start: 0.7697 (mmt) cc_final: 0.7401 (mmm) REVERT: B 236 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7393 (mmt) outliers start: 34 outliers final: 22 residues processed: 103 average time/residue: 0.1790 time to fit residues: 26.8452 Evaluate side-chains 88 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8836 Z= 0.175 Angle : 0.649 8.741 12081 Z= 0.318 Chirality : 0.041 0.144 1470 Planarity : 0.005 0.088 1538 Dihedral : 8.262 135.573 1274 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.62 % Favored : 90.20 % Rotamer: Outliers : 4.20 % Allowed : 17.05 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.26), residues: 1143 helix: 0.88 (0.20), residues: 712 sheet: -1.59 (0.61), residues: 74 loop : -3.28 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.002 0.001 HIS A 827 PHE 0.019 0.001 PHE B 334 TYR 0.006 0.001 TYR B 283 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 68 time to evaluate : 0.919 Fit side-chains REVERT: A 397 ASP cc_start: 0.8467 (m-30) cc_final: 0.8172 (m-30) REVERT: A 454 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 231 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: B 236 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7270 (mmt) outliers start: 37 outliers final: 25 residues processed: 94 average time/residue: 0.1734 time to fit residues: 24.3240 Evaluate side-chains 90 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8836 Z= 0.157 Angle : 0.634 7.767 12081 Z= 0.309 Chirality : 0.040 0.161 1470 Planarity : 0.005 0.086 1538 Dihedral : 8.105 134.222 1273 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.84 % Favored : 90.99 % Rotamer: Outliers : 3.75 % Allowed : 18.86 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.63 (0.26), residues: 1143 helix: 0.95 (0.21), residues: 711 sheet: -1.32 (0.62), residues: 74 loop : -3.10 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.002 0.000 HIS B 526 PHE 0.014 0.001 PHE A 554 TYR 0.015 0.001 TYR A 403 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 0.988 Fit side-chains REVERT: A 392 LYS cc_start: 0.9197 (tmmt) cc_final: 0.8703 (tmtt) REVERT: A 396 ASP cc_start: 0.7825 (m-30) cc_final: 0.7477 (m-30) REVERT: A 454 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 236 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7198 (mmt) outliers start: 33 outliers final: 26 residues processed: 94 average time/residue: 0.1818 time to fit residues: 25.1582 Evaluate side-chains 93 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 383 HIS ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8836 Z= 0.193 Angle : 0.638 7.584 12081 Z= 0.314 Chirality : 0.040 0.159 1470 Planarity : 0.005 0.086 1538 Dihedral : 8.030 132.978 1273 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 4.20 % Allowed : 19.32 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.46 (0.26), residues: 1143 helix: 1.06 (0.21), residues: 706 sheet: -1.26 (0.61), residues: 74 loop : -2.91 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.003 0.001 HIS A 827 PHE 0.017 0.001 PHE B 334 TYR 0.010 0.001 TYR A 425 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 0.971 Fit side-chains REVERT: A 392 LYS cc_start: 0.9205 (tmmt) cc_final: 0.8948 (tmtt) REVERT: A 454 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 231 MET cc_start: 0.7488 (mmm) cc_final: 0.7010 (mpp) REVERT: B 236 MET cc_start: 0.7884 (tmm) cc_final: 0.7237 (mmt) REVERT: B 333 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7231 (pt0) outliers start: 37 outliers final: 30 residues processed: 93 average time/residue: 0.1865 time to fit residues: 25.6018 Evaluate side-chains 92 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 61 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 0.0070 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8836 Z= 0.165 Angle : 0.632 7.671 12081 Z= 0.309 Chirality : 0.040 0.154 1470 Planarity : 0.005 0.085 1538 Dihedral : 7.948 131.859 1273 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.62 % Favored : 90.29 % Rotamer: Outliers : 4.09 % Allowed : 19.20 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.46 (0.26), residues: 1143 helix: 1.05 (0.21), residues: 710 sheet: -1.24 (0.61), residues: 74 loop : -2.96 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.002 0.000 HIS A 827 PHE 0.014 0.001 PHE B 334 TYR 0.016 0.001 TYR A 403 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9191 (tmmt) cc_final: 0.8981 (tmtt) REVERT: A 454 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 511 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8976 (pp) REVERT: B 231 MET cc_start: 0.7428 (mmm) cc_final: 0.7092 (mpp) REVERT: B 236 MET cc_start: 0.7812 (tmm) cc_final: 0.7137 (mmt) REVERT: B 333 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7271 (pt0) outliers start: 36 outliers final: 29 residues processed: 91 average time/residue: 0.1745 time to fit residues: 23.4128 Evaluate side-chains 95 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8836 Z= 0.170 Angle : 0.649 9.771 12081 Z= 0.315 Chirality : 0.040 0.154 1470 Planarity : 0.005 0.084 1538 Dihedral : 7.735 130.917 1269 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.90 % Rotamer: Outliers : 3.86 % Allowed : 19.32 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.40 (0.26), residues: 1143 helix: 1.09 (0.21), residues: 709 sheet: -1.18 (0.60), residues: 74 loop : -2.92 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.002 0.000 HIS A 827 PHE 0.014 0.001 PHE B 334 TYR 0.010 0.001 TYR A 425 ARG 0.004 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 64 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 511 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 750 GLU cc_start: 0.7581 (mp0) cc_final: 0.7345 (mp0) REVERT: B 236 MET cc_start: 0.7835 (tmm) cc_final: 0.7142 (mmt) REVERT: B 283 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8948 (t80) REVERT: B 333 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7241 (pt0) outliers start: 34 outliers final: 28 residues processed: 90 average time/residue: 0.1714 time to fit residues: 23.2848 Evaluate side-chains 95 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8836 Z= 0.150 Angle : 0.661 10.146 12081 Z= 0.314 Chirality : 0.040 0.164 1470 Planarity : 0.005 0.083 1538 Dihedral : 7.632 129.410 1269 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.49 % Favored : 91.34 % Rotamer: Outliers : 3.86 % Allowed : 19.77 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.27 (0.26), residues: 1143 helix: 1.21 (0.21), residues: 697 sheet: -1.06 (0.60), residues: 74 loop : -2.78 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.003 0.000 HIS A 582 PHE 0.009 0.001 PHE B 334 TYR 0.020 0.001 TYR A 403 ARG 0.006 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 511 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 750 GLU cc_start: 0.7533 (mp0) cc_final: 0.7329 (mp0) REVERT: B 236 MET cc_start: 0.7846 (tmm) cc_final: 0.7040 (mmt) REVERT: B 283 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8893 (t80) REVERT: B 333 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7185 (pt0) outliers start: 34 outliers final: 28 residues processed: 98 average time/residue: 0.1923 time to fit residues: 27.5785 Evaluate side-chains 99 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 0.0050 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8836 Z= 0.178 Angle : 0.671 10.764 12081 Z= 0.320 Chirality : 0.040 0.162 1470 Planarity : 0.005 0.083 1538 Dihedral : 7.571 128.250 1269 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 3.52 % Allowed : 20.23 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.23 (0.26), residues: 1143 helix: 1.23 (0.21), residues: 693 sheet: -0.84 (0.63), residues: 69 loop : -2.72 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 841 HIS 0.002 0.000 HIS B 526 PHE 0.013 0.001 PHE B 334 TYR 0.010 0.001 TYR A 425 ARG 0.006 0.000 ARG A 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.7853 (m-30) cc_final: 0.7558 (m-30) REVERT: A 454 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 511 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8986 (pp) REVERT: B 236 MET cc_start: 0.7837 (tmm) cc_final: 0.7071 (mmt) REVERT: B 283 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8926 (t80) REVERT: B 333 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7285 (pt0) outliers start: 31 outliers final: 26 residues processed: 91 average time/residue: 0.1635 time to fit residues: 22.3415 Evaluate side-chains 96 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.065691 restraints weight = 24261.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.067928 restraints weight = 12100.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.069456 restraints weight = 7779.567| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8836 Z= 0.182 Angle : 0.666 10.784 12081 Z= 0.319 Chirality : 0.041 0.159 1470 Planarity : 0.005 0.084 1538 Dihedral : 7.548 126.875 1269 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.10 % Favored : 90.64 % Rotamer: Outliers : 3.64 % Allowed : 20.00 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.20 (0.26), residues: 1143 helix: 1.22 (0.21), residues: 694 sheet: -0.75 (0.63), residues: 69 loop : -2.68 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 841 HIS 0.002 0.000 HIS A 827 PHE 0.015 0.001 PHE B 334 TYR 0.019 0.001 TYR A 403 ARG 0.006 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.90 seconds wall clock time: 33 minutes 18.36 seconds (1998.36 seconds total)