Starting phenix.real_space_refine on Sat Jul 20 01:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u53_41911/07_2024/8u53_41911.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 P 4 5.49 5 S 34 5.16 5 C 6476 2.51 5 N 1442 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 5.51, per 1000 atoms: 0.58 Number of scatterers: 9562 At special positions: 0 Unit cell: (130.81, 118.45, 90.64, 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) S 34 16.00 P 4 15.00 O 1606 8.00 N 1442 7.00 C 6476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 84.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 184 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 246 No H-bonds generated for 'chain 'A' and resid 235 through 246' Processing helix chain 'A' and resid 281 through 303 No H-bonds generated for 'chain 'A' and resid 281 through 303' Processing helix chain 'A' and resid 317 through 325 No H-bonds generated for 'chain 'A' and resid 317 through 325' Processing helix chain 'A' and resid 343 through 347 No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 348 through 352 No H-bonds generated for 'chain 'A' and resid 348 through 352' Processing helix chain 'A' and resid 355 through 377 No H-bonds generated for 'chain 'A' and resid 355 through 377' Processing helix chain 'A' and resid 377 through 388 No H-bonds generated for 'chain 'A' and resid 377 through 388' Processing helix chain 'A' and resid 411 through 415 No H-bonds generated for 'chain 'A' and resid 411 through 415' Processing helix chain 'A' and resid 416 through 427 No H-bonds generated for 'chain 'A' and resid 416 through 427' Processing helix chain 'A' and resid 428 through 439 No H-bonds generated for 'chain 'A' and resid 428 through 439' Processing helix chain 'A' and resid 444 through 463 No H-bonds generated for 'chain 'A' and resid 444 through 463' Processing helix chain 'A' and resid 464 through 474 No H-bonds generated for 'chain 'A' and resid 464 through 474' Processing helix chain 'A' and resid 490 through 498 No H-bonds generated for 'chain 'A' and resid 490 through 498' Processing helix chain 'A' and resid 501 through 523 No H-bonds generated for 'chain 'A' and resid 501 through 523' Processing helix chain 'A' and resid 523 through 537 No H-bonds generated for 'chain 'A' and resid 523 through 537' Processing helix chain 'A' and resid 540 through 549 No H-bonds generated for 'chain 'A' and resid 540 through 549' Processing helix chain 'A' and resid 554 through 573 No H-bonds generated for 'chain 'A' and resid 554 through 573' Processing helix chain 'A' and resid 578 through 601 No H-bonds generated for 'chain 'A' and resid 578 through 601' Processing helix chain 'A' and resid 612 through 638 No H-bonds generated for 'chain 'A' and resid 612 through 638' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 646 through 665 No H-bonds generated for 'chain 'A' and resid 646 through 665' Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 672 through 677 No H-bonds generated for 'chain 'A' and resid 672 through 677' Processing helix chain 'A' and resid 685 through 692 No H-bonds generated for 'chain 'A' and resid 685 through 692' Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 184 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 235 through 246 No H-bonds generated for 'chain 'B' and resid 235 through 246' Processing helix chain 'B' and resid 281 through 303 No H-bonds generated for 'chain 'B' and resid 281 through 303' Processing helix chain 'B' and resid 317 through 325 No H-bonds generated for 'chain 'B' and resid 317 through 325' Processing helix chain 'B' and resid 343 through 347 No H-bonds generated for 'chain 'B' and resid 343 through 347' Processing helix chain 'B' and resid 348 through 352 No H-bonds generated for 'chain 'B' and resid 348 through 352' Processing helix chain 'B' and resid 355 through 377 No H-bonds generated for 'chain 'B' and resid 355 through 377' Processing helix chain 'B' and resid 377 through 388 No H-bonds generated for 'chain 'B' and resid 377 through 388' Processing helix chain 'B' and resid 411 through 415 No H-bonds generated for 'chain 'B' and resid 411 through 415' Processing helix chain 'B' and resid 416 through 427 No H-bonds generated for 'chain 'B' and resid 416 through 427' Processing helix chain 'B' and resid 428 through 439 No H-bonds generated for 'chain 'B' and resid 428 through 439' Processing helix chain 'B' and resid 444 through 463 No H-bonds generated for 'chain 'B' and resid 444 through 463' Processing helix chain 'B' and resid 464 through 474 No H-bonds generated for 'chain 'B' and resid 464 through 474' Processing helix chain 'B' and resid 490 through 498 No H-bonds generated for 'chain 'B' and resid 490 through 498' Processing helix chain 'B' and resid 501 through 523 No H-bonds generated for 'chain 'B' and resid 501 through 523' Processing helix chain 'B' and resid 523 through 537 No H-bonds generated for 'chain 'B' and resid 523 through 537' Processing helix chain 'B' and resid 540 through 549 No H-bonds generated for 'chain 'B' and resid 540 through 549' Processing helix chain 'B' and resid 554 through 573 No H-bonds generated for 'chain 'B' and resid 554 through 573' Processing helix chain 'B' and resid 578 through 601 No H-bonds generated for 'chain 'B' and resid 578 through 601' Processing helix chain 'B' and resid 612 through 638 No H-bonds generated for 'chain 'B' and resid 612 through 638' Processing helix chain 'B' and resid 642 through 645 No H-bonds generated for 'chain 'B' and resid 642 through 645' Processing helix chain 'B' and resid 646 through 665 No H-bonds generated for 'chain 'B' and resid 646 through 665' Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 672 through 677 No H-bonds generated for 'chain 'B' and resid 672 through 677' Processing helix chain 'B' and resid 685 through 692 No H-bonds generated for 'chain 'B' and resid 685 through 692' Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 229 WARNING: can't find one or more strands! previous: chain 'A' and resid 226 through 229 current: chain 'A' and resid 311 through 314 WARNING: can't find one or more strands! previous: chain 'A' and resid 311 through 314 current: chain 'A' and resid 193 through 197 WARNING: can't find one or more strands! previous: chain 'A' and resid 193 through 197 current: chain 'A' and resid 337 through 340 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 229 WARNING: can't find one or more strands! previous: chain 'B' and resid 226 through 229 current: chain 'B' and resid 311 through 314 WARNING: can't find one or more strands! previous: chain 'B' and resid 311 through 314 current: chain 'B' and resid 193 through 197 WARNING: can't find one or more strands! previous: chain 'B' and resid 193 through 197 current: chain 'B' and resid 337 through 340 No H-bonds generated for sheet with id=AA2 191 hydrogen bonds defined for protein. 567 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: 2.02 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1587 1.31 - 1.44: 3076 1.44 - 1.58: 4940 1.58 - 1.71: 121 1.71 - 1.84: 60 Bond restraints: 9784 Sorted by residual: bond pdb=" O4P CPL A 801 " pdb=" P CPL A 801 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O4P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C10 82T B 803 " pdb=" C9 82T B 803 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C10 82T A 802 " pdb=" C9 82T A 802 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CB LEU B 566 " pdb=" CG LEU B 566 " ideal model delta sigma weight residual 1.530 1.397 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.21: 313 106.21 - 113.21: 4919 113.21 - 120.20: 4393 120.20 - 127.19: 3430 127.19 - 134.18: 101 Bond angle restraints: 13156 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 111.62 118.85 -7.23 7.90e-01 1.60e+00 8.38e+01 angle pdb=" N VAL A 601 " pdb=" CA VAL A 601 " pdb=" C VAL A 601 " ideal model delta sigma weight residual 111.62 118.82 -7.20 7.90e-01 1.60e+00 8.31e+01 angle pdb=" C ALA A 576 " pdb=" N PRO A 577 " pdb=" CA PRO A 577 " ideal model delta sigma weight residual 119.56 128.78 -9.22 1.02e+00 9.61e-01 8.17e+01 angle pdb=" C ALA B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " pdb=" CG PHE A 513 " ideal model delta sigma weight residual 113.80 122.41 -8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 13151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 5670 34.85 - 69.70: 120 69.70 - 104.56: 16 104.56 - 139.41: 4 139.41 - 174.26: 6 Dihedral angle restraints: 5816 sinusoidal: 2434 harmonic: 3382 Sorted by residual: dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 309.18 135.88 173.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1076 0.106 - 0.212: 319 0.212 - 0.318: 61 0.318 - 0.424: 6 0.424 - 0.530: 6 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C3 CPL A 801 " pdb=" O2 CPL A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C2 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C3 CPL B 802 " pdb=" O2 CPL B 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 1465 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " -0.068 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR A 171 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.068 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR B 171 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.045 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR B 215 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " 0.048 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5201 2.98 - 3.46: 10073 3.46 - 3.94: 16677 3.94 - 4.42: 20779 4.42 - 4.90: 29636 Nonbonded interactions: 82366 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O GLY A 667 " model vdw 2.498 2.520 nonbonded pdb=" NH1 ARG B 178 " pdb=" O GLY B 667 " model vdw 2.499 2.520 nonbonded pdb=" C SER A 501 " pdb=" OG SER A 501 " model vdw 2.534 2.616 nonbonded pdb=" C SER B 501 " pdb=" OG SER B 501 " model vdw 2.534 2.616 nonbonded pdb=" CB PLM A 809 " pdb=" CE PLM A 809 " model vdw 2.553 3.072 ... (remaining 82361 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 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) selection = (chain 'B' and (resid 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.190 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.024 0.150 9784 Z= 1.537 Angle : 1.715 16.408 13156 Z= 1.115 Chirality : 0.104 0.530 1468 Planarity : 0.009 0.036 1572 Dihedral : 15.246 174.260 3624 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.71 (0.24), residues: 1054 helix: 0.53 (0.17), residues: 742 sheet: None (None), residues: 0 loop : 0.70 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP A 336 HIS 0.006 0.002 HIS A 696 PHE 0.037 0.007 PHE A 513 TYR 0.068 0.009 TYR A 171 ARG 0.008 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7298 (tt0) cc_final: 0.7037 (tt0) REVERT: B 343 GLU cc_start: 0.7362 (tt0) cc_final: 0.7078 (tt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0756 time to fit residues: 208.3654 Evaluate side-chains 121 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9784 Z= 0.217 Angle : 0.557 9.359 13156 Z= 0.296 Chirality : 0.041 0.182 1468 Planarity : 0.004 0.038 1572 Dihedral : 17.649 176.486 1666 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.26 % Allowed : 7.53 % Favored : 90.22 % 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: 1.51 (0.25), residues: 1054 helix: 1.15 (0.18), residues: 740 sheet: None (None), residues: 0 loop : 0.97 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 336 HIS 0.003 0.001 HIS A 329 PHE 0.037 0.002 PHE A 513 TYR 0.020 0.002 TYR B 536 ARG 0.002 0.000 ARG B 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 0.965 Fit side-chains REVERT: A 428 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.3898 (tmt) outliers start: 21 outliers final: 5 residues processed: 150 average time/residue: 0.9561 time to fit residues: 156.4817 Evaluate side-chains 117 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 100 optimal weight: 0.0870 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9784 Z= 0.237 Angle : 0.551 7.793 13156 Z= 0.285 Chirality : 0.040 0.170 1468 Planarity : 0.005 0.037 1572 Dihedral : 16.522 174.477 1666 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 10.00 % Favored : 87.20 % 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: 1.27 (0.25), residues: 1054 helix: 1.09 (0.18), residues: 740 sheet: None (None), residues: 0 loop : 0.53 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 548 HIS 0.005 0.001 HIS B 447 PHE 0.032 0.002 PHE B 513 TYR 0.016 0.002 TYR A 171 ARG 0.010 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.996 Fit side-chains REVERT: B 428 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4155 (tmt) outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 0.8419 time to fit residues: 122.7681 Evaluate side-chains 123 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0170 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 90 optimal weight: 5.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9784 Z= 0.140 Angle : 0.463 6.928 13156 Z= 0.240 Chirality : 0.038 0.142 1468 Planarity : 0.004 0.037 1572 Dihedral : 15.871 173.362 1666 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 11.08 % Favored : 87.31 % 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: 1.83 (0.25), residues: 1054 helix: 1.46 (0.18), residues: 720 sheet: None (None), residues: 0 loop : 0.90 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 548 HIS 0.002 0.001 HIS B 447 PHE 0.025 0.001 PHE A 513 TYR 0.013 0.001 TYR A 225 ARG 0.005 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.911 Fit side-chains REVERT: A 161 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7334 (mp) REVERT: A 428 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4317 (tmt) REVERT: B 428 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4188 (tmt) outliers start: 15 outliers final: 4 residues processed: 131 average time/residue: 1.0214 time to fit residues: 145.6542 Evaluate side-chains 120 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9784 Z= 0.378 Angle : 0.626 6.115 13156 Z= 0.323 Chirality : 0.044 0.173 1468 Planarity : 0.005 0.037 1572 Dihedral : 16.620 170.794 1666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.80 % Allowed : 11.40 % Favored : 85.81 % 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: 0.61 (0.25), residues: 1054 helix: 0.60 (0.18), residues: 732 sheet: None (None), residues: 0 loop : 0.27 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 548 HIS 0.010 0.002 HIS A 447 PHE 0.035 0.003 PHE A 513 TYR 0.018 0.002 TYR A 634 ARG 0.006 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.967 Fit side-chains REVERT: A 222 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5735 (tt0) REVERT: A 410 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.6464 (pmt170) REVERT: A 428 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.4305 (tmt) REVERT: B 222 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: B 410 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.6436 (pmt170) REVERT: B 428 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4300 (tmt) outliers start: 26 outliers final: 10 residues processed: 142 average time/residue: 1.0351 time to fit residues: 159.3062 Evaluate side-chains 132 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 554 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9784 Z= 0.228 Angle : 0.511 5.858 13156 Z= 0.265 Chirality : 0.039 0.152 1468 Planarity : 0.004 0.039 1572 Dihedral : 16.312 169.739 1666 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.47 % Allowed : 12.90 % Favored : 84.62 % 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: 0.85 (0.25), residues: 1054 helix: 0.82 (0.18), residues: 732 sheet: None (None), residues: 0 loop : 0.22 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 548 HIS 0.005 0.001 HIS A 447 PHE 0.030 0.002 PHE B 513 TYR 0.012 0.001 TYR A 225 ARG 0.003 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.984 Fit side-chains REVERT: A 222 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5669 (tt0) REVERT: A 410 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.6475 (pmt170) REVERT: A 428 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.4300 (tmt) REVERT: B 410 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.6481 (pmt170) outliers start: 23 outliers final: 12 residues processed: 136 average time/residue: 1.0872 time to fit residues: 159.6265 Evaluate side-chains 135 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.0030 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9784 Z= 0.137 Angle : 0.451 6.087 13156 Z= 0.231 Chirality : 0.037 0.138 1468 Planarity : 0.004 0.036 1572 Dihedral : 15.705 168.755 1666 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.51 % Allowed : 14.41 % Favored : 84.09 % 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: 1.42 (0.26), residues: 1054 helix: 1.27 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.43 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 548 HIS 0.002 0.001 HIS B 447 PHE 0.025 0.001 PHE B 513 TYR 0.009 0.001 TYR B 157 ARG 0.003 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.009 Fit side-chains REVERT: A 410 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6473 (pmt170) REVERT: A 428 MET cc_start: 0.5326 (OUTLIER) cc_final: 0.4679 (tmt) REVERT: B 410 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.6475 (pmt170) outliers start: 14 outliers final: 4 residues processed: 137 average time/residue: 1.0980 time to fit residues: 162.3132 Evaluate side-chains 124 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9784 Z= 0.178 Angle : 0.487 7.092 13156 Z= 0.250 Chirality : 0.038 0.145 1468 Planarity : 0.004 0.035 1572 Dihedral : 15.726 167.676 1666 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.72 % Allowed : 14.62 % 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: 1.42 (0.26), residues: 1054 helix: 1.19 (0.19), residues: 736 sheet: None (None), residues: 0 loop : 0.62 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 548 HIS 0.004 0.001 HIS A 447 PHE 0.026 0.001 PHE B 513 TYR 0.010 0.001 TYR A 634 ARG 0.003 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.884 Fit side-chains REVERT: A 410 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.6476 (pmt170) REVERT: A 428 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.4748 (tmt) REVERT: B 410 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.6479 (pmt170) REVERT: B 428 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4332 (tmt) outliers start: 16 outliers final: 7 residues processed: 131 average time/residue: 1.0196 time to fit residues: 144.8064 Evaluate side-chains 125 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.218 Angle : 0.520 7.275 13156 Z= 0.268 Chirality : 0.039 0.151 1468 Planarity : 0.004 0.035 1572 Dihedral : 15.917 167.952 1666 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.83 % Allowed : 14.84 % Favored : 83.33 % 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: 1.25 (0.26), residues: 1054 helix: 1.12 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.41 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 548 HIS 0.005 0.001 HIS A 447 PHE 0.029 0.002 PHE B 513 TYR 0.018 0.001 TYR A 225 ARG 0.003 0.000 ARG B 595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.896 Fit side-chains REVERT: A 410 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.6491 (pmt170) REVERT: B 410 ARG cc_start: 0.7569 (ttp-170) cc_final: 0.6492 (pmt170) REVERT: B 428 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4723 (tmt) outliers start: 17 outliers final: 7 residues processed: 131 average time/residue: 1.0458 time to fit residues: 148.8809 Evaluate side-chains 127 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9784 Z= 0.325 Angle : 0.595 7.429 13156 Z= 0.306 Chirality : 0.042 0.159 1468 Planarity : 0.005 0.038 1572 Dihedral : 16.477 169.188 1666 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.97 % Allowed : 15.70 % Favored : 83.33 % 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: 0.61 (0.25), residues: 1054 helix: 0.67 (0.19), residues: 732 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 548 HIS 0.008 0.002 HIS B 447 PHE 0.034 0.002 PHE A 513 TYR 0.016 0.002 TYR A 225 ARG 0.004 0.001 ARG A 595 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.964 Fit side-chains REVERT: A 222 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5632 (tt0) REVERT: A 410 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.6500 (pmt170) REVERT: B 410 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.6509 (pmt170) outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 1.1126 time to fit residues: 151.0288 Evaluate side-chains 125 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 554 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110950 restraints weight = 14247.339| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.82 r_work: 0.3458 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9784 Z= 0.142 Angle : 0.480 7.401 13156 Z= 0.245 Chirality : 0.038 0.140 1468 Planarity : 0.004 0.036 1572 Dihedral : 15.819 166.628 1666 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.86 % Allowed : 15.70 % Favored : 83.44 % 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: 1.25 (0.26), residues: 1054 helix: 1.15 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.33 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 548 HIS 0.002 0.001 HIS A 447 PHE 0.026 0.001 PHE B 513 TYR 0.009 0.001 TYR B 157 ARG 0.003 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3385.80 seconds wall clock time: 60 minutes 3.51 seconds (3603.51 seconds total)