Starting phenix.real_space_refine on Tue Nov 14 18:36:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8k_30306/11_2023/7c8k_30306.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4459 atoms to isotropic. 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 Zn 1 6.06 5 S 29 5.16 5 C 3104 2.51 5 N 804 2.21 5 O 915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 4853 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4782 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.18, per 1000 atoms: 0.66 Number of scatterers: 4853 At special positions: 0 Unit cell: (78.5062, 87.45, 79.5, 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) Zn 1 29.99 S 29 16.00 O 915 8.00 N 804 7.00 C 3104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 706 " - " ASN A 329 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 892.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 705 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 374 " 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 66.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.564A pdb=" N GLU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.688A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.690A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.573A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.639A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.557A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.698A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.772A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.119A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.521A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.953A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.717A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.705A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.652A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.562A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 258 hydrogen bonds defined for protein. 753 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: 1.38 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1541 1.34 - 1.46: 1058 1.46 - 1.58: 2340 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 4989 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG A 706 " pdb=" O5 NAG A 706 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 4984 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 220 107.35 - 114.01: 2730 114.01 - 120.67: 2159 120.67 - 127.33: 1579 127.33 - 133.99: 85 Bond angle restraints: 6773 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.71 109.31 4.40 9.50e-01 1.11e+00 2.15e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.22 109.12 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 122.21 130.81 -8.60 2.87e+00 1.21e-01 8.99e+00 angle pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta sigma weight residual 121.62 125.48 -3.86 1.57e+00 4.06e-01 6.04e+00 angle pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N LEU A 108 " ideal model delta sigma weight residual 119.87 116.80 3.07 1.34e+00 5.57e-01 5.24e+00 ... (remaining 6768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2655 17.16 - 34.33: 209 34.33 - 51.49: 36 51.49 - 68.65: 6 68.65 - 85.81: 10 Dihedral angle restraints: 2916 sinusoidal: 1168 harmonic: 1748 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.47 38.47 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CB GLU A 208 " pdb=" CG GLU A 208 " pdb=" CD GLU A 208 " pdb=" OE1 GLU A 208 " ideal model delta sinusoidal sigma weight residual 0.00 -83.89 83.89 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 2913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 719 0.134 - 0.267: 2 0.267 - 0.401: 0 0.401 - 0.535: 0 0.535 - 0.668: 1 Chirality restraints: 722 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.12e+03 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 719 not shown) Planarity restraints: 865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 583 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 146 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.55e-01 pdb=" N PRO A 235 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.014 5.00e-02 4.00e+02 ... (remaining 862 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 3919 3.16 - 3.74: 7832 3.74 - 4.32: 10681 4.32 - 4.90: 17675 Nonbonded interactions: 40145 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 705 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 227 " pdb=" OH TYR A 454 " model vdw 2.295 2.440 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.298 2.440 nonbonded pdb=" O TRP A 48 " pdb=" OG1 THR A 52 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.303 2.440 ... (remaining 40140 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 1.120 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.002 0.029 4989 Z= 0.149 Angle : 0.515 8.603 6773 Z= 0.293 Chirality : 0.045 0.668 722 Planarity : 0.003 0.041 861 Dihedral : 13.618 85.814 1783 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.52 (0.31), residues: 594 helix: -0.16 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2033 time to fit residues: 24.3569 Evaluate side-chains 51 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4989 Z= 0.131 Angle : 0.470 6.537 6773 Z= 0.230 Chirality : 0.039 0.180 722 Planarity : 0.004 0.053 861 Dihedral : 2.872 11.323 646 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.40 % Allowed : 7.60 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.34), residues: 594 helix: 1.14 (0.28), residues: 357 sheet: -2.69 (1.11), residues: 12 loop : -1.64 (0.36), residues: 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.1180 time to fit residues: 9.7408 Evaluate side-chains 52 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0469 time to fit residues: 0.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4989 Z= 0.146 Angle : 0.469 6.508 6773 Z= 0.230 Chirality : 0.039 0.124 722 Planarity : 0.004 0.054 861 Dihedral : 3.053 12.583 646 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.60 % Allowed : 9.80 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.70 (0.34), residues: 594 helix: 1.64 (0.28), residues: 360 sheet: -2.36 (1.21), residues: 12 loop : -1.37 (0.37), residues: 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.1206 time to fit residues: 9.7853 Evaluate side-chains 49 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0479 time to fit residues: 0.8666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.0030 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4989 Z= 0.127 Angle : 0.458 6.434 6773 Z= 0.225 Chirality : 0.039 0.174 722 Planarity : 0.003 0.053 861 Dihedral : 3.057 12.635 646 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.20 % Allowed : 10.80 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.15 (0.35), residues: 594 helix: 1.97 (0.28), residues: 356 sheet: -2.30 (1.19), residues: 12 loop : -1.07 (0.38), residues: 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1292 time to fit residues: 9.8184 Evaluate side-chains 49 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0772 time to fit residues: 0.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4989 Z= 0.227 Angle : 0.522 6.732 6773 Z= 0.263 Chirality : 0.041 0.165 722 Planarity : 0.004 0.056 861 Dihedral : 3.489 13.495 646 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.40 % Allowed : 12.80 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.17 (0.35), residues: 594 helix: 1.77 (0.28), residues: 368 sheet: -2.13 (1.21), residues: 12 loop : -0.81 (0.40), residues: 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.1205 time to fit residues: 9.1067 Evaluate side-chains 43 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 41 optimal weight: 6.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4989 Z= 0.150 Angle : 0.489 6.517 6773 Z= 0.243 Chirality : 0.039 0.175 722 Planarity : 0.004 0.053 861 Dihedral : 3.337 14.351 646 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.40 % Allowed : 13.20 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.28 (0.35), residues: 594 helix: 1.89 (0.28), residues: 367 sheet: -2.20 (1.18), residues: 12 loop : -0.80 (0.40), residues: 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.1203 time to fit residues: 9.3153 Evaluate side-chains 47 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0631 time to fit residues: 1.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.0000 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4989 Z= 0.141 Angle : 0.473 6.695 6773 Z= 0.235 Chirality : 0.039 0.158 722 Planarity : 0.004 0.052 861 Dihedral : 3.254 13.280 646 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.40 % Allowed : 13.60 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.43 (0.35), residues: 594 helix: 1.98 (0.28), residues: 368 sheet: -2.29 (1.16), residues: 12 loop : -0.67 (0.40), residues: 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.1204 time to fit residues: 8.9187 Evaluate side-chains 45 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0467 time to fit residues: 0.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4989 Z= 0.143 Angle : 0.473 6.820 6773 Z= 0.235 Chirality : 0.039 0.149 722 Planarity : 0.004 0.052 861 Dihedral : 3.228 13.211 646 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.80 % Allowed : 13.00 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.45 (0.35), residues: 594 helix: 2.03 (0.28), residues: 367 sheet: -2.30 (1.17), residues: 12 loop : -0.74 (0.40), residues: 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.1291 time to fit residues: 9.0818 Evaluate side-chains 45 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0503 time to fit residues: 0.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4989 Z= 0.136 Angle : 0.480 6.846 6773 Z= 0.237 Chirality : 0.039 0.152 722 Planarity : 0.004 0.051 861 Dihedral : 3.189 13.063 646 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.52 (0.35), residues: 594 helix: 2.08 (0.28), residues: 367 sheet: -2.36 (1.17), residues: 12 loop : -0.68 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1162 time to fit residues: 8.2725 Evaluate side-chains 45 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4989 Z= 0.146 Angle : 0.475 6.849 6773 Z= 0.236 Chirality : 0.039 0.154 722 Planarity : 0.004 0.052 861 Dihedral : 3.186 12.712 646 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.59 (0.35), residues: 594 helix: 2.11 (0.28), residues: 369 sheet: -2.48 (1.14), residues: 12 loop : -0.61 (0.41), residues: 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1502 time to fit residues: 10.1087 Evaluate side-chains 44 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.101376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.084225 restraints weight = 9867.712| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.26 r_work: 0.3121 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4989 Z= 0.138 Angle : 0.477 7.448 6773 Z= 0.235 Chirality : 0.039 0.149 722 Planarity : 0.004 0.051 861 Dihedral : 3.165 12.884 646 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 13.60 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.64 (0.35), residues: 594 helix: 2.14 (0.28), residues: 369 sheet: -2.33 (1.18), residues: 12 loop : -0.60 (0.41), residues: 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.26 seconds wall clock time: 24 minutes 27.39 seconds (1467.39 seconds total)