Starting phenix.real_space_refine on Thu Mar 14 17:51:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7c_11677/03_2024/7a7c_11677_updated.pdb" } resolution = 3.16 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= 0.012 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 1 7.16 5 S 32 5.16 5 C 5973 2.51 5 N 1622 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ASP 735": "OD1" <-> "OD2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 515": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B GLU 703": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4277 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 30, 'TRANS': 529} Chain breaks: 4 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5110 Unusual residues: {'HEM': 1} Classifications: {'peptide': 666, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 43, 'TRANS': 622, None: 1} Not linked: pdbres="VAL B 739 " pdbres="HEM B 801 " Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 5.59, per 1000 atoms: 0.60 Number of scatterers: 9387 At special positions: 0 Unit cell: (84.76, 96.496, 126.488, 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 1 26.01 S 32 16.00 O 1759 8.00 N 1622 7.00 C 5973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 2.0 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 3 sheets defined 46.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.995A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.254A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.574A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.830A pdb=" N MET A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.520A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 453 through 461 Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.581A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 503 No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 540 through 559 removed outlier: 3.719A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 removed outlier: 4.423A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.920A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 693 through 700 removed outlier: 4.443A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.767A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.753A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.648A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.510A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.024A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.176A pdb=" N LEU B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 399 removed outlier: 3.648A pdb=" N ARG B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.818A pdb=" N SER B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 493 through 498 removed outlier: 4.424A pdb=" N ARG B 496 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 497 " --> pdb=" O GLY B 494 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 493 through 498' Processing helix chain 'B' and resid 500 through 503 No H-bonds generated for 'chain 'B' and resid 500 through 503' Processing helix chain 'B' and resid 515 through 530 Processing helix chain 'B' and resid 540 through 559 removed outlier: 3.795A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 634 removed outlier: 3.905A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 693 through 700 removed outlier: 4.264A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.815A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 Processing sheet with id= A, first strand: chain 'A' and resid 667 through 670 removed outlier: 3.538A pdb=" N THR A 667 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 341 through 344 Processing sheet with id= C, first strand: chain 'B' and resid 667 through 670 305 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3928 1.39 - 1.56: 5636 1.56 - 1.72: 0 1.72 - 1.89: 60 1.89 - 2.05: 4 Bond restraints: 9628 Sorted by residual: bond pdb=" CA TRP B 39 " pdb=" C TRP B 39 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.26e-01 bond pdb=" CA TRP B 351 " pdb=" C TRP B 351 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 7.06e-01 bond pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 6.65e-01 bond pdb=" CA PRO B 239 " pdb=" C PRO B 239 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 6.49e-01 bond pdb=" CA ASP A 240 " pdb=" C ASP A 240 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.00e-01 ... (remaining 9623 not shown) Histogram of bond angle deviations from ideal: 88.93 - 106.93: 366 106.93 - 124.94: 12492 124.94 - 142.95: 262 142.95 - 160.95: 0 160.95 - 178.96: 2 Bond angle restraints: 13122 Sorted by residual: angle pdb=" N PRO B 642 " pdb=" CA PRO B 642 " pdb=" C PRO B 642 " ideal model delta sigma weight residual 114.68 111.41 3.27 1.04e+00 9.25e-01 9.86e+00 angle pdb=" N ILE A 462 " pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 111.91 109.66 2.25 8.90e-01 1.26e+00 6.37e+00 angle pdb=" CA TYR B 597 " pdb=" C TYR B 597 " pdb=" N LEU B 598 " ideal model delta sigma weight residual 114.81 118.16 -3.35 1.42e+00 4.96e-01 5.56e+00 angle pdb=" N TYR B 597 " pdb=" CA TYR B 597 " pdb=" C TYR B 597 " ideal model delta sigma weight residual 111.17 113.92 -2.75 1.41e+00 5.03e-01 3.80e+00 angle pdb=" CA PRO B 642 " pdb=" C PRO B 642 " pdb=" O PRO B 642 " ideal model delta sigma weight residual 118.92 121.13 -2.21 1.14e+00 7.69e-01 3.77e+00 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5129 17.94 - 35.88: 413 35.88 - 53.82: 65 53.82 - 71.76: 11 71.76 - 89.70: 9 Dihedral angle restraints: 5627 sinusoidal: 2163 harmonic: 3464 Sorted by residual: dihedral pdb=" CA ARG B 595 " pdb=" C ARG B 595 " pdb=" N ASN B 596 " pdb=" CA ASN B 596 " ideal model delta harmonic sigma weight residual 180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA B 130 " pdb=" C ALA B 130 " pdb=" N PRO B 131 " pdb=" CA PRO B 131 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N GLU B 340 " pdb=" CA GLU B 340 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.052: 404 0.052 - 0.077: 173 0.077 - 0.103: 64 0.103 - 0.129: 14 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" C PRO B 367 " pdb=" CB PRO B 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 666 " pdb=" N ILE B 666 " pdb=" C ILE B 666 " pdb=" CB ILE B 666 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE B 364 " pdb=" N ILE B 364 " pdb=" C ILE B 364 " pdb=" CB ILE B 364 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 1409 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 279 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 280 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 509 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 510 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 604 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 605 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.021 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 860 2.74 - 3.28: 9591 3.28 - 3.82: 15292 3.82 - 4.36: 18637 4.36 - 4.90: 32026 Nonbonded interactions: 76406 Sorted by model distance: nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR B 113 " pdb=" OD2 ASP B 487 " model vdw 2.236 2.440 nonbonded pdb=" O VAL A 267 " pdb=" OG1 THR A 271 " model vdw 2.256 2.440 nonbonded pdb=" O GLY A 599 " pdb=" ND2 ASN A 602 " model vdw 2.265 2.520 nonbonded pdb=" O TYR B 390 " pdb=" OG1 THR B 394 " model vdw 2.272 2.440 ... (remaining 76401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.600 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.290 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.003 0.050 9628 Z= 0.204 Angle : 0.538 7.175 13122 Z= 0.295 Chirality : 0.039 0.129 1412 Planarity : 0.004 0.081 1722 Dihedral : 13.508 89.701 3413 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1210 helix: 0.27 (0.22), residues: 568 sheet: -1.66 (1.18), residues: 21 loop : -1.50 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 689 HIS 0.005 0.001 HIS A 49 PHE 0.013 0.001 PHE B 129 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2101 time to fit residues: 21.6765 Evaluate side-chains 52 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9628 Z= 0.357 Angle : 0.547 7.561 13122 Z= 0.270 Chirality : 0.042 0.125 1412 Planarity : 0.004 0.068 1722 Dihedral : 4.966 65.495 1324 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.53 % Allowed : 7.01 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1210 helix: 0.36 (0.22), residues: 572 sheet: -1.44 (1.11), residues: 21 loop : -1.57 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 341 HIS 0.005 0.001 HIS A 49 PHE 0.011 0.001 PHE B 724 TYR 0.014 0.001 TYR B 597 ARG 0.004 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 1.140 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.2014 time to fit residues: 16.1557 Evaluate side-chains 47 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9628 Z= 0.157 Angle : 0.469 7.203 13122 Z= 0.227 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.057 1722 Dihedral : 4.611 71.556 1324 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.32 % Allowed : 8.28 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1210 helix: 0.73 (0.23), residues: 574 sheet: -0.73 (1.17), residues: 21 loop : -1.46 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 689 HIS 0.005 0.001 HIS A 49 PHE 0.009 0.001 PHE B 129 TYR 0.010 0.001 TYR B 597 ARG 0.002 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.173 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1835 time to fit residues: 17.0626 Evaluate side-chains 49 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9628 Z= 0.290 Angle : 0.517 7.748 13122 Z= 0.251 Chirality : 0.040 0.120 1412 Planarity : 0.004 0.054 1722 Dihedral : 4.737 67.508 1324 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1210 helix: 0.73 (0.22), residues: 567 sheet: -0.49 (1.18), residues: 21 loop : -1.46 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE B 724 TYR 0.012 0.001 TYR B 597 ARG 0.003 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 1.085 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1803 time to fit residues: 15.5093 Evaluate side-chains 51 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9628 Z= 0.207 Angle : 0.486 7.151 13122 Z= 0.234 Chirality : 0.038 0.121 1412 Planarity : 0.004 0.050 1722 Dihedral : 4.619 70.619 1324 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.74 % Allowed : 11.15 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1210 helix: 0.85 (0.22), residues: 568 sheet: -0.19 (1.22), residues: 21 loop : -1.43 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 351 HIS 0.004 0.001 HIS A 49 PHE 0.007 0.001 PHE B 129 TYR 0.010 0.001 TYR B 597 ARG 0.002 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 1.072 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 0.1837 time to fit residues: 16.7858 Evaluate side-chains 50 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9628 Z= 0.149 Angle : 0.469 7.220 13122 Z= 0.224 Chirality : 0.037 0.121 1412 Planarity : 0.003 0.046 1722 Dihedral : 4.424 72.842 1324 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.74 % Allowed : 11.46 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1210 helix: 1.02 (0.23), residues: 576 sheet: 0.04 (1.23), residues: 21 loop : -1.35 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.003 0.000 HIS A 49 PHE 0.006 0.001 PHE B 129 TYR 0.009 0.001 TYR B 597 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 1.159 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.1821 time to fit residues: 16.7976 Evaluate side-chains 50 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9628 Z= 0.174 Angle : 0.480 7.712 13122 Z= 0.230 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.046 1722 Dihedral : 4.426 72.228 1324 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.74 % Allowed : 12.00 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1210 helix: 1.06 (0.22), residues: 576 sheet: 0.18 (1.23), residues: 21 loop : -1.34 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.004 0.000 HIS A 49 PHE 0.006 0.001 PHE A 167 TYR 0.019 0.001 TYR B 98 ARG 0.002 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.093 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.1780 time to fit residues: 15.8603 Evaluate side-chains 51 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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: 0.8435 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9628 Z= 0.160 Angle : 0.477 7.078 13122 Z= 0.227 Chirality : 0.037 0.120 1412 Planarity : 0.003 0.045 1722 Dihedral : 4.389 73.061 1324 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.74 % Allowed : 12.31 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1210 helix: 1.15 (0.22), residues: 576 sheet: -0.29 (1.00), residues: 33 loop : -1.35 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.005 0.000 HIS A 49 PHE 0.005 0.001 PHE B 129 TYR 0.028 0.001 TYR B 98 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 1.181 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.1799 time to fit residues: 15.5505 Evaluate side-chains 52 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9628 Z= 0.223 Angle : 0.503 8.584 13122 Z= 0.242 Chirality : 0.039 0.119 1412 Planarity : 0.004 0.046 1722 Dihedral : 4.497 71.293 1324 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.85 % Allowed : 12.63 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1210 helix: 1.11 (0.22), residues: 572 sheet: -0.26 (0.99), residues: 33 loop : -1.38 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.004 0.001 HIS A 49 PHE 0.007 0.001 PHE B 724 TYR 0.024 0.001 TYR B 98 ARG 0.002 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.148 Fit side-chains REVERT: B 732 MET cc_start: 0.8832 (mmp) cc_final: 0.8488 (mmp) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.1871 time to fit residues: 17.0025 Evaluate side-chains 56 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9628 Z= 0.180 Angle : 0.494 8.013 13122 Z= 0.237 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.045 1722 Dihedral : 4.452 72.635 1324 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.64 % Allowed : 13.16 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1210 helix: 1.18 (0.22), residues: 575 sheet: -0.23 (0.99), residues: 33 loop : -1.37 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 397 HIS 0.004 0.000 HIS A 49 PHE 0.006 0.001 PHE A 167 TYR 0.021 0.001 TYR B 98 ARG 0.002 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: B 732 MET cc_start: 0.8819 (mmp) cc_final: 0.8519 (mmp) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.1852 time to fit residues: 16.6193 Evaluate side-chains 55 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083717 restraints weight = 16865.760| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.43 r_work: 0.3012 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9628 Z= 0.170 Angle : 0.496 11.014 13122 Z= 0.235 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.044 1722 Dihedral : 4.385 73.190 1324 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.74 % Allowed : 13.16 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1210 helix: 1.23 (0.22), residues: 576 sheet: -0.16 (0.99), residues: 33 loop : -1.36 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 351 HIS 0.004 0.000 HIS A 49 PHE 0.008 0.001 PHE A 129 TYR 0.019 0.001 TYR B 98 ARG 0.002 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.19 seconds wall clock time: 33 minutes 16.87 seconds (1996.87 seconds total)