Starting phenix.real_space_refine on Tue Feb 13 10:05:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fei_29028/02_2024/8fei_29028.pdb" } resolution = 3.0 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= 0.026 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 Fe 2 7.16 5 S 41 5.16 5 C 3242 2.51 5 N 901 2.21 5 O 1003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 659": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5189 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5189 Unusual residues: {' FE': 2} Inner-chain residues flagged as termini: ['pdbres="LYS A 686 "'] Classifications: {'peptide': 674, 'undetermined': 2} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 649, None: 2} Not linked: pdbres="LYS A 686 " pdbres=" FE A 701 " Not linked: pdbres=" FE A 701 " pdbres=" FE A 702 " Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 3.38, per 1000 atoms: 0.65 Number of scatterers: 5189 At special positions: 0 Unit cell: (63.356, 74.14, 105.144, 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) Fe 2 26.01 S 41 16.00 O 1003 8.00 N 901 7.00 C 3242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 45 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 36 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 371 " distance=2.01 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 680 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 584 " distance=2.03 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 39.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.676A pdb=" N LEU A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.917A pdb=" N GLU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.639A pdb=" N LEU A 109 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN A 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 110' Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.839A pdb=" N ALA A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.513A pdb=" N ARG A 172 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.285A pdb=" N CYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.647A pdb=" N PHE A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 217 removed outlier: 3.691A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 258 through 275 removed outlier: 4.484A pdb=" N ASP A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 3.682A pdb=" N LEU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.649A pdb=" N ALA A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.507A pdb=" N LYS A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.639A pdb=" N ILE A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.725A pdb=" N TYR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.985A pdb=" N GLY A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.727A pdb=" N LEU A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 616 removed outlier: 3.679A pdb=" N ILE A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.799A pdb=" N GLY A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.573A pdb=" N CYS A 680 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 6.106A pdb=" N ILE A 7 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 37 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP A 9 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.686A pdb=" N ILE A 57 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 78 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 254 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A 306 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.518A pdb=" N SER A 114 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 113 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE A 207 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 115 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS A 209 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 208 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA A 96 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.518A pdb=" N SER A 114 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 113 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE A 207 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 115 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS A 209 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 208 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 245 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.662A pdb=" N ILE A 345 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THR A 372 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP A 347 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 374 " --> pdb=" O TRP A 347 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 349 " --> pdb=" O VAL A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 removed outlier: 3.882A pdb=" N VAL A 392 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 594 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A 643 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 541 removed outlier: 4.668A pdb=" N ALA A 435 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 570 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG A 574 " --> pdb=" O CYS A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 541 removed outlier: 3.732A pdb=" N ALA A 587 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 removed outlier: 7.349A pdb=" N SER A 453 " --> pdb=" O CYS A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 177 hydrogen bonds defined for protein. 510 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: 1.60 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1168 1.33 - 1.45: 1125 1.45 - 1.57: 2943 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 5288 Sorted by residual: bond pdb=" N ILE A 57 " pdb=" CA ILE A 57 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N LEU A 299 " pdb=" CA LEU A 299 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N VAL A 596 " pdb=" CA VAL A 596 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.22e-02 6.72e+03 9.68e+00 bond pdb=" N LYS A 181 " pdb=" CA LYS A 181 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.85e+00 bond pdb=" N PHE A 300 " pdb=" CA PHE A 300 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.13e-02 7.83e+03 7.83e+00 ... (remaining 5283 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.63: 131 106.63 - 113.54: 2906 113.54 - 120.44: 2031 120.44 - 127.35: 2029 127.35 - 134.25: 46 Bond angle restraints: 7143 Sorted by residual: angle pdb=" O TYR A 191 " pdb=" C TYR A 191 " pdb=" N SER A 192 " ideal model delta sigma weight residual 122.07 116.43 5.64 1.03e+00 9.43e-01 3.00e+01 angle pdb=" CA TYR A 191 " pdb=" C TYR A 191 " pdb=" N SER A 192 " ideal model delta sigma weight residual 117.07 122.99 -5.92 1.14e+00 7.69e-01 2.69e+01 angle pdb=" C LEU A 635 " pdb=" N LEU A 636 " pdb=" CA LEU A 636 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" N TYR A 191 " ideal model delta sigma weight residual 114.69 121.23 -6.54 1.43e+00 4.89e-01 2.09e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 122.57 118.47 4.10 9.20e-01 1.18e+00 1.98e+01 ... (remaining 7138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 2854 15.57 - 31.13: 272 31.13 - 46.70: 83 46.70 - 62.27: 13 62.27 - 77.83: 13 Dihedral angle restraints: 3235 sinusoidal: 1298 harmonic: 1937 Sorted by residual: dihedral pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 160.73 -67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS A 570 " pdb=" SG CYS A 570 " pdb=" SG CYS A 584 " pdb=" CB CYS A 584 " ideal model delta sinusoidal sigma weight residual -86.00 -143.26 57.26 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " pdb=" SG CYS A 643 " pdb=" CB CYS A 643 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 ... (remaining 3232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 617 0.059 - 0.119: 135 0.119 - 0.178: 23 0.178 - 0.238: 4 0.238 - 0.297: 1 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA GLU A 370 " pdb=" N GLU A 370 " pdb=" C GLU A 370 " pdb=" CB GLU A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 596 " pdb=" N VAL A 596 " pdb=" C VAL A 596 " pdb=" CB VAL A 596 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 777 not shown) Planarity restraints: 933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 190 " 0.014 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C GLY A 190 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY A 190 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 191 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 292 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO A 293 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 298 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU A 298 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 298 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 299 " -0.012 2.00e-02 2.50e+03 ... (remaining 930 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 6 2.21 - 2.88: 1985 2.88 - 3.56: 7083 3.56 - 4.23: 12448 4.23 - 4.90: 20680 Nonbonded interactions: 42202 Sorted by model distance: nonbonded pdb=" OH TYR A 191 " pdb="FE FE A 701 " model vdw 1.541 2.260 nonbonded pdb=" OD2 ASP A 395 " pdb="FE FE A 702 " model vdw 1.984 2.260 nonbonded pdb=" OH TYR A 524 " pdb="FE FE A 702 " model vdw 2.039 2.260 nonbonded pdb=" NE2 HIS A 250 " pdb="FE FE A 701 " model vdw 2.089 2.340 nonbonded pdb=" OH TYR A 92 " pdb="FE FE A 701 " model vdw 2.098 2.260 ... (remaining 42197 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.000 Extract box with map and model: 6.770 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.007 0.039 5288 Z= 0.433 Angle : 0.914 9.190 7143 Z= 0.605 Chirality : 0.053 0.297 780 Planarity : 0.005 0.054 933 Dihedral : 13.997 77.834 1946 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.98 (0.24), residues: 670 helix: -3.97 (0.16), residues: 211 sheet: -2.64 (0.48), residues: 74 loop : -1.81 (0.26), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.006 0.001 HIS A 210 PHE 0.011 0.002 PHE A 645 TYR 0.020 0.002 TYR A 191 ARG 0.004 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.676 Fit side-chains REVERT: A 679 MET cc_start: 0.8740 (ppp) cc_final: 0.8540 (ppp) REVERT: A 684 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7789 (pp20) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 2.0299 time to fit residues: 76.2453 Evaluate side-chains 17 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 51 ASN A 63 GLN A 500 GLN A 541 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5288 Z= 0.232 Angle : 0.545 5.995 7143 Z= 0.291 Chirality : 0.040 0.158 780 Planarity : 0.004 0.034 933 Dihedral : 4.769 26.544 725 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.89 % Allowed : 11.25 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.23 (0.28), residues: 670 helix: -1.75 (0.28), residues: 210 sheet: -2.52 (0.46), residues: 84 loop : -0.95 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.002 0.001 HIS A 196 PHE 0.010 0.001 PHE A 195 TYR 0.012 0.001 TYR A 431 ARG 0.006 0.001 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.658 Fit side-chains REVERT: A 306 MET cc_start: 0.8675 (ttm) cc_final: 0.8452 (tpt) REVERT: A 684 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7703 (pp20) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 1.2098 time to fit residues: 31.0748 Evaluate side-chains 17 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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: 0.8297 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5288 Z= 0.194 Angle : 0.499 8.331 7143 Z= 0.263 Chirality : 0.040 0.136 780 Planarity : 0.003 0.029 933 Dihedral : 4.316 17.707 723 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.07 % Allowed : 11.25 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 670 helix: -0.50 (0.32), residues: 212 sheet: -2.37 (0.48), residues: 84 loop : -0.55 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE A 628 TYR 0.010 0.001 TYR A 431 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.655 Fit side-chains REVERT: A 306 MET cc_start: 0.8639 (ttm) cc_final: 0.8418 (tpt) REVERT: A 684 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7673 (pp20) outliers start: 6 outliers final: 1 residues processed: 23 average time/residue: 1.1386 time to fit residues: 27.9605 Evaluate side-chains 17 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5288 Z= 0.208 Angle : 0.497 8.123 7143 Z= 0.260 Chirality : 0.040 0.135 780 Planarity : 0.003 0.027 933 Dihedral : 4.236 16.624 723 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.43 % Allowed : 12.50 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.31), residues: 670 helix: 0.14 (0.35), residues: 212 sheet: -2.34 (0.47), residues: 87 loop : -0.29 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 196 PHE 0.022 0.001 PHE A 266 TYR 0.010 0.001 TYR A 191 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.635 Fit side-chains REVERT: A 306 MET cc_start: 0.8650 (ttm) cc_final: 0.8425 (tpt) REVERT: A 411 MET cc_start: 0.8739 (mtp) cc_final: 0.8494 (mmt) REVERT: A 684 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7720 (pp20) outliers start: 8 outliers final: 2 residues processed: 23 average time/residue: 1.2525 time to fit residues: 30.7428 Evaluate side-chains 18 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 16 optimal weight: 0.0040 chunk 21 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5288 Z= 0.105 Angle : 0.441 8.409 7143 Z= 0.230 Chirality : 0.038 0.119 780 Planarity : 0.003 0.025 933 Dihedral : 3.885 16.011 723 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.07 % Allowed : 14.29 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.32), residues: 670 helix: 0.44 (0.36), residues: 213 sheet: -2.05 (0.50), residues: 87 loop : -0.28 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.003 0.001 HIS A 592 PHE 0.008 0.001 PHE A 645 TYR 0.008 0.001 TYR A 431 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.623 Fit side-chains REVERT: A 306 MET cc_start: 0.8607 (ttm) cc_final: 0.8376 (tpt) REVERT: A 684 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7619 (pp20) outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 1.2260 time to fit residues: 32.7515 Evaluate side-chains 18 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.6444 ------------------------------------------------------------------------------- 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: 0.8297 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5288 Z= 0.210 Angle : 0.501 9.283 7143 Z= 0.258 Chirality : 0.040 0.128 780 Planarity : 0.003 0.025 933 Dihedral : 4.003 16.170 723 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.89 % Allowed : 14.64 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.33), residues: 670 helix: 0.77 (0.37), residues: 212 sheet: -1.99 (0.50), residues: 87 loop : -0.07 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.002 0.001 HIS A 196 PHE 0.026 0.001 PHE A 266 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.610 Fit side-chains REVERT: A 306 MET cc_start: 0.8649 (ttm) cc_final: 0.8415 (tpt) REVERT: A 626 MET cc_start: 0.8141 (mmm) cc_final: 0.7663 (tpp) REVERT: A 684 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7736 (pp20) outliers start: 5 outliers final: 2 residues processed: 21 average time/residue: 1.2482 time to fit residues: 28.1140 Evaluate side-chains 18 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5288 Z= 0.120 Angle : 0.476 10.368 7143 Z= 0.240 Chirality : 0.039 0.138 780 Planarity : 0.003 0.025 933 Dihedral : 3.817 15.520 723 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.71 % Allowed : 14.46 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.33), residues: 670 helix: 0.91 (0.37), residues: 212 sheet: -1.86 (0.51), residues: 87 loop : -0.05 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.002 0.001 HIS A 592 PHE 0.009 0.001 PHE A 645 TYR 0.012 0.001 TYR A 431 ARG 0.001 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.610 Fit side-chains REVERT: A 306 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8397 (tpt) REVERT: A 626 MET cc_start: 0.8041 (mmm) cc_final: 0.7697 (tpp) REVERT: A 684 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7649 (pp20) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 1.2886 time to fit residues: 26.3245 Evaluate side-chains 19 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5288 Z= 0.246 Angle : 0.527 11.106 7143 Z= 0.269 Chirality : 0.041 0.139 780 Planarity : 0.003 0.026 933 Dihedral : 4.044 16.062 723 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.89 % Allowed : 15.18 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.34), residues: 670 helix: 1.10 (0.38), residues: 212 sheet: -1.90 (0.51), residues: 87 loop : 0.06 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.002 0.001 HIS A 542 PHE 0.031 0.001 PHE A 266 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.649 Fit side-chains REVERT: A 306 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (ttm) REVERT: A 626 MET cc_start: 0.7987 (mmm) cc_final: 0.7224 (tpp) REVERT: A 684 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7820 (pp20) outliers start: 5 outliers final: 2 residues processed: 19 average time/residue: 1.2340 time to fit residues: 25.2651 Evaluate side-chains 18 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 0.0040 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- 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: 0.8261 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 0.024 5288 Z= 0.117 Angle : 0.484 11.737 7143 Z= 0.242 Chirality : 0.039 0.124 780 Planarity : 0.003 0.025 933 Dihedral : 3.792 15.262 723 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.54 % Allowed : 16.07 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.34), residues: 670 helix: 1.20 (0.37), residues: 213 sheet: -1.83 (0.52), residues: 87 loop : 0.06 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.003 0.001 HIS A 592 PHE 0.009 0.001 PHE A 645 TYR 0.011 0.001 TYR A 431 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.553 Fit side-chains REVERT: A 306 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8411 (tpt) REVERT: A 626 MET cc_start: 0.7842 (mmm) cc_final: 0.7151 (tpp) REVERT: A 684 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7693 (pp20) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 1.2625 time to fit residues: 28.3663 Evaluate side-chains 20 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8294 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5288 Z= 0.221 Angle : 0.526 12.003 7143 Z= 0.267 Chirality : 0.041 0.125 780 Planarity : 0.003 0.025 933 Dihedral : 3.973 15.745 723 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.89 % Allowed : 15.71 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.34), residues: 670 helix: 1.26 (0.37), residues: 213 sheet: -1.90 (0.51), residues: 87 loop : 0.12 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.002 0.001 HIS A 196 PHE 0.041 0.002 PHE A 300 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.608 Fit side-chains REVERT: A 306 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8423 (ttm) REVERT: A 626 MET cc_start: 0.7800 (mmm) cc_final: 0.7151 (tpp) REVERT: A 684 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7819 (pp20) outliers start: 5 outliers final: 2 residues processed: 21 average time/residue: 1.0962 time to fit residues: 24.8896 Evaluate side-chains 19 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.060800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049394 restraints weight = 18831.576| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.25 r_work: 0.2800 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5288 Z= 0.135 Angle : 0.502 12.135 7143 Z= 0.251 Chirality : 0.039 0.125 780 Planarity : 0.003 0.026 933 Dihedral : 3.837 16.847 723 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.54 % Allowed : 16.25 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.34), residues: 670 helix: 1.38 (0.37), residues: 211 sheet: -1.98 (0.49), residues: 93 loop : 0.14 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.002 0.001 HIS A 592 PHE 0.037 0.001 PHE A 300 TYR 0.011 0.001 TYR A 431 ARG 0.001 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.67 seconds wall clock time: 30 minutes 55.39 seconds (1855.39 seconds total)