Starting phenix.real_space_refine on Thu Mar 14 23:48:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a7a_11676/03_2024/7a7a_11676_updated.pdb" } resolution = 3.08 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 34 5.16 5 C 6450 2.51 5 N 1739 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 487": "OD1" <-> "OD2" 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 582": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B ASP 735": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5000 Classifications: {'peptide': 657} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 40, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5061 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 43, 'TRANS': 623} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.59 Number of scatterers: 10147 At special positions: 0 Unit cell: (84.76, 95.192, 125.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 34 16.00 O 1922 8.00 N 1739 7.00 C 6450 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 1.9 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 2 sheets defined 41.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 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: 3.557A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 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 110 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.487A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 245 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 271 Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 383 through 386 No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.807A pdb=" N ARG A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 417 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 454 through 463 Processing helix chain 'A' and resid 469 through 480 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 531 removed outlier: 3.675A pdb=" N ARG A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 removed outlier: 3.787A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 621 through 633 removed outlier: 4.033A 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 702 through 711 removed outlier: 3.974A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 734 removed outlier: 3.536A pdb=" N VAL A 721 " --> pdb=" O GLN A 717 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) 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 68 Processing helix chain 'B' and resid 73 through 84 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 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' 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 142 through 147 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.666A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LYS B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 175 removed outlier: 3.563A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 4.035A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 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 332 through 336 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 388 through 398 removed outlier: 4.704A 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 452 through 463 removed outlier: 3.510A pdb=" N ALA B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 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 removed outlier: 3.910A pdb=" N ILE B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 556 removed outlier: 3.798A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 621 through 633 removed outlier: 3.747A 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: 4.412A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 711 removed outlier: 4.178A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 Processing sheet with id= A, first strand: chain 'B' and resid 341 through 345 Processing sheet with id= B, first strand: chain 'B' and resid 667 through 670 280 hydrogen bonds defined for protein. 831 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: 2.42 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 4260 1.39 - 1.55: 6092 1.55 - 1.72: 1 1.72 - 1.88: 64 1.88 - 2.05: 8 Bond restraints: 10425 Sorted by residual: bond pdb=" CB TRP B 397 " pdb=" CG TRP B 397 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.37e+00 bond pdb=" CG LEU B 298 " pdb=" CD1 LEU B 298 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" CB ASN B 655 " pdb=" CG ASN B 655 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CG LEU B 141 " pdb=" CD1 LEU B 141 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CG LEU A 543 " pdb=" CD1 LEU A 543 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 ... (remaining 10420 not shown) Histogram of bond angle deviations from ideal: 89.00 - 107.02: 430 107.02 - 125.05: 13468 125.05 - 143.08: 342 143.08 - 161.11: 0 161.11 - 179.14: 4 Bond angle restraints: 14244 Sorted by residual: angle pdb=" C THR A 275 " pdb=" N HIS A 276 " pdb=" CA HIS A 276 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N GLY A 683 " pdb=" CA GLY A 683 " pdb=" C GLY A 683 " ideal model delta sigma weight residual 113.18 104.39 8.79 2.37e+00 1.78e-01 1.38e+01 angle pdb=" N THR A 376 " pdb=" CA THR A 376 " pdb=" C THR A 376 " ideal model delta sigma weight residual 108.65 113.64 -4.99 1.85e+00 2.92e-01 7.27e+00 angle pdb=" C LEU A 543 " pdb=" N VAL A 544 " pdb=" CA VAL A 544 " ideal model delta sigma weight residual 120.56 117.30 3.26 1.26e+00 6.30e-01 6.71e+00 angle pdb=" CA LEU A 696 " pdb=" CB LEU A 696 " pdb=" CG LEU A 696 " ideal model delta sigma weight residual 116.30 125.10 -8.80 3.50e+00 8.16e-02 6.32e+00 ... (remaining 14239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5518 17.93 - 35.87: 438 35.87 - 53.80: 76 53.80 - 71.73: 8 71.73 - 89.66: 12 Dihedral angle restraints: 6052 sinusoidal: 2321 harmonic: 3731 Sorted by residual: dihedral pdb=" CA ASP A 682 " pdb=" C ASP A 682 " pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" N THR A 376 " pdb=" CA THR A 376 " ideal model delta harmonic sigma weight residual -180.00 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 775 0.035 - 0.070: 521 0.070 - 0.105: 170 0.105 - 0.140: 42 0.140 - 0.175: 7 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA GLN A 500 " pdb=" N GLN A 500 " pdb=" C GLN A 500 " pdb=" CB GLN A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CG LEU B 499 " pdb=" CB LEU B 499 " pdb=" CD1 LEU B 499 " pdb=" CD2 LEU B 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA GLN B 500 " pdb=" N GLN B 500 " pdb=" C GLN B 500 " pdb=" CB GLN B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1512 not shown) Planarity restraints: 1874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 370 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO A 371 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 149 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO A 150 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 509 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 510 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.028 5.00e-02 4.00e+02 ... (remaining 1871 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 600 2.71 - 3.26: 10435 3.26 - 3.81: 16317 3.81 - 4.35: 20913 4.35 - 4.90: 35703 Nonbonded interactions: 83968 Sorted by model distance: nonbonded pdb=" O TRP A 341 " pdb=" NE2 GLN A 352 " model vdw 2.167 2.520 nonbonded pdb=" NH2 ARG B 249 " pdb=" OD2 ASP B 387 " model vdw 2.191 2.520 nonbonded pdb=" O THR A 275 " pdb=" ND1 HIS A 276 " model vdw 2.195 2.520 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.248 2.440 nonbonded pdb=" O SER B 140 " pdb=" OG SER B 140 " model vdw 2.251 2.440 ... (remaining 83963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 165 or (resid 166 and (name N or n \ ame CA or name C or name O or name CB )) or resid 167 through 178 or (resid 179 \ and (name N or name CA or name C or name O or name CB )) or resid 180 through 19 \ 6 or resid 240 through 326 or (resid 327 and (name N or name CA or name C or nam \ e O or name CB )) or resid 328 through 515 or (resid 516 and (name N or name CA \ or name C or name O or name CB )) or resid 517 through 536 or (resid 537 and (na \ me N or name CA or name C or name O or name CB )) or resid 538 through 589 or (r \ esid 590 through 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 739 or resid 801)) selection = (chain 'B' and (resid 40 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 193 or (resid 194 through 195 and \ (name N or name CA or name C or name O or name CB )) or resid 196 or resid 240 t \ hrough 252 or (resid 253 and (name N or name CA or name C or name O or name CB ) \ ) or resid 254 through 282 or (resid 283 and (name N or name CA or name C or nam \ e O or name CB )) or resid 284 through 286 or (resid 287 and (name N or name CA \ or name C or name O or name CB )) or resid 288 through 341 or (resid 342 through \ 343 and (name N or name CA or name C or name O or name CB )) or resid 344 throu \ gh 346 or resid 351 through 352 or (resid 353 and (name N or name CA or name C o \ r name O or name CB )) or resid 354 through 367 or (resid 368 and (name N or nam \ e CA or name C or name O or name CB )) or resid 369 through 739 or resid 801)) } 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: 0.010 Normalize map: mean=0, sd=1: 2.960 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: 11.480 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.110 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.009 0.082 10425 Z= 0.590 Angle : 0.755 8.799 14244 Z= 0.394 Chirality : 0.049 0.175 1515 Planarity : 0.005 0.053 1874 Dihedral : 13.719 89.664 3674 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.22), residues: 1314 helix: -0.81 (0.21), residues: 544 sheet: -1.46 (1.24), residues: 20 loop : -1.79 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 39 HIS 0.008 0.002 HIS A 276 PHE 0.023 0.002 PHE B 332 TYR 0.018 0.002 TYR A 155 ARG 0.008 0.001 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2387 time to fit residues: 28.0606 Evaluate side-chains 72 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.0000 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10425 Z= 0.167 Angle : 0.556 12.640 14244 Z= 0.267 Chirality : 0.040 0.129 1515 Planarity : 0.005 0.054 1874 Dihedral : 5.571 67.129 1436 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.59 % Allowed : 4.92 % Favored : 94.49 % 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: -1.50 (0.22), residues: 1314 helix: -0.23 (0.22), residues: 551 sheet: -0.55 (1.29), residues: 20 loop : -1.65 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.005 0.001 HIS A 276 PHE 0.011 0.001 PHE B 657 TYR 0.012 0.001 TYR A 155 ARG 0.004 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.182 Fit side-chains REVERT: A 137 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7064 (p0) REVERT: B 513 ASP cc_start: 0.7191 (p0) cc_final: 0.6991 (p0) outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.2117 time to fit residues: 29.6497 Evaluate side-chains 87 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 116 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN B 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10425 Z= 0.340 Angle : 0.603 14.122 14244 Z= 0.288 Chirality : 0.043 0.140 1515 Planarity : 0.005 0.055 1874 Dihedral : 5.694 69.821 1436 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.79 % Allowed : 8.66 % Favored : 90.55 % 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: -1.47 (0.22), residues: 1314 helix: -0.19 (0.22), residues: 554 sheet: -0.76 (1.29), residues: 20 loop : -1.64 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 90 HIS 0.007 0.001 HIS A 276 PHE 0.016 0.001 PHE B 332 TYR 0.018 0.001 TYR A 304 ARG 0.004 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.167 Fit side-chains REVERT: A 137 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7038 (p0) outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 0.2244 time to fit residues: 27.3700 Evaluate side-chains 81 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10425 Z= 0.195 Angle : 0.534 12.582 14244 Z= 0.252 Chirality : 0.040 0.130 1515 Planarity : 0.004 0.051 1874 Dihedral : 5.286 67.597 1436 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.89 % Allowed : 10.63 % Favored : 88.48 % 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: -1.21 (0.23), residues: 1314 helix: 0.11 (0.23), residues: 548 sheet: -0.78 (1.18), residues: 20 loop : -1.56 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 90 HIS 0.006 0.001 HIS A 276 PHE 0.007 0.001 PHE B 332 TYR 0.013 0.001 TYR A 155 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.249 Fit side-chains REVERT: A 137 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7030 (p0) REVERT: B 612 ASP cc_start: 0.7790 (t70) cc_final: 0.7561 (t0) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.2076 time to fit residues: 26.8571 Evaluate side-chains 85 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10425 Z= 0.274 Angle : 0.564 13.184 14244 Z= 0.266 Chirality : 0.042 0.132 1515 Planarity : 0.004 0.048 1874 Dihedral : 5.385 69.190 1436 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.38 % Allowed : 12.01 % Favored : 86.61 % 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: -1.22 (0.22), residues: 1314 helix: 0.10 (0.23), residues: 551 sheet: -0.85 (1.16), residues: 20 loop : -1.56 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 90 HIS 0.007 0.001 HIS A 276 PHE 0.012 0.001 PHE B 332 TYR 0.017 0.001 TYR A 155 ARG 0.003 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.150 Fit side-chains REVERT: A 137 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 612 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7617 (t0) outliers start: 14 outliers final: 9 residues processed: 89 average time/residue: 0.2116 time to fit residues: 27.6230 Evaluate side-chains 90 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 695 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10425 Z= 0.168 Angle : 0.517 11.906 14244 Z= 0.243 Chirality : 0.039 0.131 1515 Planarity : 0.004 0.050 1874 Dihedral : 5.077 67.138 1436 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.67 % Allowed : 12.89 % Favored : 85.43 % 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: -0.99 (0.23), residues: 1314 helix: 0.37 (0.23), residues: 549 sheet: -0.64 (1.10), residues: 20 loop : -1.50 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.005 0.000 HIS A 276 PHE 0.006 0.001 PHE B 272 TYR 0.012 0.001 TYR A 155 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.117 Fit side-chains REVERT: A 137 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6977 (p0) REVERT: B 612 ASP cc_start: 0.7843 (t70) cc_final: 0.7604 (t0) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.2119 time to fit residues: 30.1691 Evaluate side-chains 93 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10425 Z= 0.165 Angle : 0.514 11.665 14244 Z= 0.241 Chirality : 0.039 0.144 1515 Planarity : 0.004 0.044 1874 Dihedral : 5.023 67.736 1436 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.48 % Allowed : 13.98 % Favored : 84.55 % 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: -0.86 (0.23), residues: 1314 helix: 0.51 (0.23), residues: 549 sheet: -0.54 (1.09), residues: 20 loop : -1.46 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.005 0.000 HIS A 276 PHE 0.006 0.001 PHE A 129 TYR 0.013 0.001 TYR A 155 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.196 Fit side-chains REVERT: A 137 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6957 (p0) REVERT: B 612 ASP cc_start: 0.7812 (t70) cc_final: 0.7578 (t0) outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 0.2157 time to fit residues: 28.8093 Evaluate side-chains 90 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.0040 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 0.0470 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10425 Z= 0.146 Angle : 0.508 11.257 14244 Z= 0.238 Chirality : 0.039 0.145 1515 Planarity : 0.004 0.044 1874 Dihedral : 4.881 66.792 1436 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.28 % Allowed : 14.17 % Favored : 84.55 % 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: -0.72 (0.23), residues: 1314 helix: 0.65 (0.23), residues: 549 sheet: -0.17 (1.12), residues: 20 loop : -1.41 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 90 HIS 0.005 0.000 HIS A 276 PHE 0.006 0.001 PHE B 272 TYR 0.012 0.001 TYR A 155 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.098 Fit side-chains REVERT: A 137 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7004 (p0) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.2263 time to fit residues: 31.5532 Evaluate side-chains 90 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10425 Z= 0.185 Angle : 0.526 11.675 14244 Z= 0.248 Chirality : 0.040 0.150 1515 Planarity : 0.004 0.046 1874 Dihedral : 4.939 67.527 1436 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.48 % Allowed : 14.86 % Favored : 83.66 % 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: -0.73 (0.23), residues: 1314 helix: 0.63 (0.23), residues: 550 sheet: -0.08 (1.12), residues: 20 loop : -1.40 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.005 0.001 HIS A 276 PHE 0.006 0.001 PHE B 657 TYR 0.013 0.001 TYR A 155 ARG 0.004 0.000 ARG B 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.229 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.2024 time to fit residues: 27.4398 Evaluate side-chains 92 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 86 optimal weight: 0.0040 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10425 Z= 0.146 Angle : 0.512 11.224 14244 Z= 0.241 Chirality : 0.039 0.146 1515 Planarity : 0.004 0.047 1874 Dihedral : 4.817 66.303 1436 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.28 % Allowed : 15.06 % Favored : 83.66 % 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: -0.60 (0.23), residues: 1314 helix: 0.81 (0.23), residues: 544 sheet: 0.03 (1.13), residues: 20 loop : -1.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 135 HIS 0.004 0.000 HIS A 276 PHE 0.006 0.001 PHE A 129 TYR 0.012 0.001 TYR A 155 ARG 0.002 0.000 ARG A 595 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.176 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.2121 time to fit residues: 29.0562 Evaluate side-chains 91 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099270 restraints weight = 15628.931| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.95 r_work: 0.3183 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10425 Z= 0.181 Angle : 0.528 11.682 14244 Z= 0.251 Chirality : 0.040 0.137 1515 Planarity : 0.004 0.047 1874 Dihedral : 4.890 67.276 1436 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.28 % Allowed : 14.86 % Favored : 83.86 % 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: -0.66 (0.23), residues: 1314 helix: 0.68 (0.23), residues: 554 sheet: -0.12 (1.11), residues: 20 loop : -1.37 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 135 HIS 0.005 0.000 HIS A 276 PHE 0.006 0.001 PHE B 657 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG B 640 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.48 seconds wall clock time: 38 minutes 40.43 seconds (2320.43 seconds total)