Starting phenix.real_space_refine (version: dev) on Sun Dec 11 15:22:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/12_2022/7sp1_25364.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 4343 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "P" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 1, 'RNA': 9} Modifications used: {'5*END': 1, 'rna3p_pur': 9} Link IDs: {'rna3p': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 1, 'RNA': 9} Modifications used: {'5*END': 1, 'rna3p_pur': 9} Link IDs: {'rna3p': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "C" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "D" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "E" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "F" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "H" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "I" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "J" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "K" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "M" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "N" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "O" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Time building chain proxies: 3.07, per 1000 atoms: 0.71 Number of scatterers: 4343 At special positions: 0 Unit cell: (81.62, 69.96, 58.3, 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 15 16.00 P 18 15.00 O 965 8.00 N 750 7.00 C 2595 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: 2.11 Conformation dependent library (CDL) restraints added in 627.4 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 41.7% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 392 through 393 removed outlier: 6.779A pdb=" N ILE A 392 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 392 " --> pdb=" O VAL H 393 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 392 " --> pdb=" O VAL K 393 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE K 392 " --> pdb=" O VAL M 393 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE M 392 " --> pdb=" O VAL O 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 399 through 403 removed outlier: 5.910A pdb=" N SER E 400 " --> pdb=" O GLY I 401 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR I 403 " --> pdb=" O SER E 400 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP E 402 " --> pdb=" O THR I 403 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER A 400 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP A 402 " --> pdb=" O THR E 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 407 through 412 removed outlier: 6.157A pdb=" N HIS E 407 " --> pdb=" O LEU I 408 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN I 410 " --> pdb=" O HIS E 407 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER E 409 " --> pdb=" O ASN I 410 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER I 412 " --> pdb=" O SER E 409 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 411 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS A 407 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASN E 410 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 409 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER E 412 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 411 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 415 through 420 removed outlier: 6.215A pdb=" N GLY A 415 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP D 418 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 417 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL D 420 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 419 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY D 415 " --> pdb=" O SER H 416 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP H 418 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 417 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL H 420 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET D 419 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY H 415 " --> pdb=" O SER K 416 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP K 418 " --> pdb=" O GLY H 415 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE H 417 " --> pdb=" O ASP K 418 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL K 420 " --> pdb=" O ILE H 417 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET H 419 " --> pdb=" O VAL K 420 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY K 415 " --> pdb=" O SER M 416 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP M 418 " --> pdb=" O GLY K 415 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE K 417 " --> pdb=" O ASP M 418 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 420 " --> pdb=" O ILE K 417 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET K 419 " --> pdb=" O VAL M 420 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY M 415 " --> pdb=" O SER O 416 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP O 418 " --> pdb=" O GLY M 415 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE M 417 " --> pdb=" O ASP O 418 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL O 420 " --> pdb=" O ILE M 417 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET M 419 " --> pdb=" O VAL O 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 392 through 393 removed outlier: 6.805A pdb=" N ILE B 392 " --> pdb=" O VAL F 393 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE F 392 " --> pdb=" O VAL J 393 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE J 392 " --> pdb=" O VAL L 393 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE L 392 " --> pdb=" O VAL N 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 399 through 403 removed outlier: 5.913A pdb=" N SER C 400 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR G 403 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP C 402 " --> pdb=" O THR G 403 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER B 400 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR C 403 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 402 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 407 through 412 removed outlier: 6.158A pdb=" N HIS C 407 " --> pdb=" O LEU G 408 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASN G 410 " --> pdb=" O HIS C 407 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER C 409 " --> pdb=" O ASN G 410 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER G 412 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 411 " --> pdb=" O SER G 412 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS B 407 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASN C 410 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 409 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER C 412 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 411 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 415 through 420 removed outlier: 6.226A pdb=" N GLY B 415 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP F 418 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 417 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL F 420 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET B 419 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY F 415 " --> pdb=" O SER J 416 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP J 418 " --> pdb=" O GLY F 415 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE F 417 " --> pdb=" O ASP J 418 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL J 420 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET F 419 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY J 415 " --> pdb=" O SER L 416 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP L 418 " --> pdb=" O GLY J 415 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE J 417 " --> pdb=" O ASP L 418 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL L 420 " --> pdb=" O ILE J 417 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET J 419 " --> pdb=" O VAL L 420 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY L 415 " --> pdb=" O SER N 416 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP N 418 " --> pdb=" O GLY L 415 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE L 417 " --> pdb=" O ASP N 418 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL N 420 " --> pdb=" O ILE L 417 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET L 419 " --> pdb=" O VAL N 420 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1090 1.33 - 1.45: 830 1.45 - 1.57: 2469 1.57 - 1.68: 36 1.68 - 1.80: 30 Bond restraints: 4455 Sorted by residual: bond pdb=" N ARG G 406 " pdb=" CA ARG G 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.85e+00 bond pdb=" N ARG C 406 " pdb=" CA ARG C 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.85e+00 bond pdb=" N ARG N 406 " pdb=" CA ARG N 406 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.23e-02 6.61e+03 9.76e+00 bond pdb=" N ARG I 406 " pdb=" CA ARG I 406 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.23e-02 6.61e+03 9.69e+00 bond pdb=" N ARG A 406 " pdb=" CA ARG A 406 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.23e-02 6.61e+03 9.68e+00 ... (remaining 4450 not shown) Histogram of bond angle deviations from ideal: 100.82 - 107.31: 381 107.31 - 113.80: 2619 113.80 - 120.29: 1411 120.29 - 126.78: 1626 126.78 - 133.27: 123 Bond angle restraints: 6160 Sorted by residual: angle pdb=" N ARG F 406 " pdb=" CA ARG F 406 " pdb=" C ARG F 406 " ideal model delta sigma weight residual 111.36 117.05 -5.69 1.09e+00 8.42e-01 2.72e+01 angle pdb=" N ARG N 406 " pdb=" CA ARG N 406 " pdb=" C ARG N 406 " ideal model delta sigma weight residual 111.36 117.04 -5.68 1.09e+00 8.42e-01 2.72e+01 angle pdb=" N ARG I 406 " pdb=" CA ARG I 406 " pdb=" C ARG I 406 " ideal model delta sigma weight residual 111.36 117.03 -5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N ARG D 406 " pdb=" CA ARG D 406 " pdb=" C ARG D 406 " ideal model delta sigma weight residual 111.36 117.03 -5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" N ARG C 406 " pdb=" CA ARG C 406 " pdb=" C ARG C 406 " ideal model delta sigma weight residual 111.36 117.02 -5.66 1.09e+00 8.42e-01 2.70e+01 ... (remaining 6155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.35: 2451 24.35 - 48.71: 218 48.71 - 73.06: 15 73.06 - 97.41: 2 97.41 - 121.76: 16 Dihedral angle restraints: 2702 sinusoidal: 1142 harmonic: 1560 Sorted by residual: dihedral pdb=" CA SER K 416 " pdb=" C SER K 416 " pdb=" N ILE K 417 " pdb=" CA ILE K 417 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER N 416 " pdb=" C SER N 416 " pdb=" N ILE N 417 " pdb=" CA ILE N 417 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 364 0.037 - 0.075: 207 0.075 - 0.112: 120 0.112 - 0.149: 46 0.149 - 0.187: 28 Chirality restraints: 765 Sorted by residual: chirality pdb=" C4' A Q 13 " pdb=" C5' A Q 13 " pdb=" O4' A Q 13 " pdb=" C3' A Q 13 " both_signs ideal model delta sigma weight residual False -2.50 -2.31 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" C4' A P 14 " pdb=" C5' A P 14 " pdb=" O4' A P 14 " pdb=" C3' A P 14 " both_signs ideal model delta sigma weight residual False -2.50 -2.31 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" C4' A Q 14 " pdb=" C5' A Q 14 " pdb=" O4' A Q 14 " pdb=" C3' A Q 14 " both_signs ideal model delta sigma weight residual False -2.50 -2.32 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 762 not shown) Planarity restraints: 723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 404 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C SER G 404 " -0.030 2.00e-02 2.50e+03 pdb=" O SER G 404 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO G 405 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 404 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C SER E 404 " 0.030 2.00e-02 2.50e+03 pdb=" O SER E 404 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO E 405 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 404 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C SER H 404 " 0.030 2.00e-02 2.50e+03 pdb=" O SER H 404 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO H 405 " -0.010 2.00e-02 2.50e+03 ... (remaining 720 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 958 2.81 - 3.33: 3845 3.33 - 3.86: 8097 3.86 - 4.38: 7893 4.38 - 4.90: 17425 Nonbonded interactions: 38218 Sorted by model distance: nonbonded pdb=" OP1 A P 11 " pdb=" NH2 ARG N 406 " model vdw 2.288 2.520 nonbonded pdb=" O2' A P 11 " pdb=" NE2 HIS L 407 " model vdw 2.342 2.520 nonbonded pdb=" OP1 A P 11 " pdb=" CZ ARG N 406 " model vdw 2.441 3.270 nonbonded pdb=" O SER H 422 " pdb=" OG SER H 422 " model vdw 2.483 2.440 nonbonded pdb=" O SER G 422 " pdb=" OG SER G 422 " model vdw 2.483 2.440 ... (remaining 38213 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 15 5.16 5 C 2595 2.51 5 N 750 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.090 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: 0.910 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.900 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.006 0.039 4455 Z= 0.399 Angle : 1.288 7.086 6160 Z= 0.781 Chirality : 0.065 0.187 765 Planarity : 0.008 0.033 723 Dihedral : 19.389 121.762 1682 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.00 % 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: -2.42 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.518 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1536 time to fit residues: 28.3178 Evaluate side-chains 108 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.031 4455 Z= 0.450 Angle : 0.915 6.473 6160 Z= 0.479 Chirality : 0.056 0.181 765 Planarity : 0.007 0.035 723 Dihedral : 21.772 123.962 767 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 3.03 % 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: -2.86 (0.35), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.528 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 0.1596 time to fit residues: 26.8320 Evaluate side-chains 111 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0462 time to fit residues: 1.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4455 Z= 0.189 Angle : 0.707 5.887 6160 Z= 0.361 Chirality : 0.046 0.151 765 Planarity : 0.006 0.027 723 Dihedral : 20.995 121.449 767 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 2.42 % 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: -2.62 (0.36), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.541 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.1653 time to fit residues: 23.7295 Evaluate side-chains 104 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0482 time to fit residues: 1.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 50.0000 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.047 4455 Z= 0.531 Angle : 0.930 7.155 6160 Z= 0.481 Chirality : 0.056 0.188 765 Planarity : 0.007 0.044 723 Dihedral : 21.423 123.546 767 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer Outliers : 2.63 % 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: -3.11 (0.35), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.520 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 0.1475 time to fit residues: 24.4392 Evaluate side-chains 117 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0532 time to fit residues: 1.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 4455 Z= 0.295 Angle : 0.784 5.598 6160 Z= 0.403 Chirality : 0.050 0.179 765 Planarity : 0.005 0.028 723 Dihedral : 21.070 125.371 767 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer Outliers : 1.41 % 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: -3.27 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.532 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 118 average time/residue: 0.1600 time to fit residues: 23.8248 Evaluate side-chains 110 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0664 time to fit residues: 1.1078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 4455 Z= 0.445 Angle : 0.872 7.156 6160 Z= 0.449 Chirality : 0.053 0.181 765 Planarity : 0.006 0.037 723 Dihedral : 21.189 125.686 767 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer Outliers : 2.42 % 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: -3.66 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.534 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 127 average time/residue: 0.1487 time to fit residues: 24.1034 Evaluate side-chains 124 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0451 time to fit residues: 1.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 4455 Z= 0.370 Angle : 0.827 6.595 6160 Z= 0.424 Chirality : 0.052 0.180 765 Planarity : 0.006 0.030 723 Dihedral : 20.977 123.011 767 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer Outliers : 2.42 % 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: -3.82 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.25), residues: 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.537 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 121 average time/residue: 0.1498 time to fit residues: 23.0017 Evaluate side-chains 118 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0523 time to fit residues: 1.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 50.0000 chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 4455 Z= 0.298 Angle : 0.780 6.252 6160 Z= 0.400 Chirality : 0.051 0.207 765 Planarity : 0.006 0.030 723 Dihedral : 20.750 121.963 767 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer Outliers : 1.82 % 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: -3.91 (0.32), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.539 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.1541 time to fit residues: 23.3529 Evaluate side-chains 118 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0570 time to fit residues: 1.0350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 overall best weight: 6.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 4455 Z= 0.385 Angle : 0.826 6.758 6160 Z= 0.426 Chirality : 0.053 0.194 765 Planarity : 0.006 0.032 723 Dihedral : 20.821 122.962 767 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer Outliers : 2.02 % 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: -4.07 (0.32), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.24), residues: 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.527 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.1570 time to fit residues: 24.0505 Evaluate side-chains 121 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0471 time to fit residues: 1.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 4455 Z= 0.360 Angle : 0.810 6.612 6160 Z= 0.418 Chirality : 0.052 0.235 765 Planarity : 0.006 0.031 723 Dihedral : 20.715 122.041 767 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Rotamer Outliers : 1.01 % 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: -4.13 (0.31), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.477 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 0.1624 time to fit residues: 24.4100 Evaluate side-chains 122 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0531 time to fit residues: 1.0359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 HIS ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5477 r_free = 0.5477 target = 0.233920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.192270 restraints weight = 4373.580| |-----------------------------------------------------------------------------| r_work (start): 0.5067 rms_B_bonded: 2.70 r_work: 0.4906 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 4455 Z= 0.296 Angle : 0.767 6.318 6160 Z= 0.393 Chirality : 0.050 0.208 765 Planarity : 0.005 0.029 723 Dihedral : 20.534 121.509 767 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Rotamer Outliers : 0.20 % 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: -4.13 (0.31), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 510 =============================================================================== Job complete usr+sys time: 1086.48 seconds wall clock time: 20 minutes 35.73 seconds (1235.73 seconds total)