Starting phenix.real_space_refine on Mon Sep 23 17:55:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/09_2024/7sp1_25364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/09_2024/7sp1_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_25364/09_2024/7sp1_25364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/09_2024/7sp1_25364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/09_2024/7sp1_25364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp1_25364/09_2024/7sp1_25364.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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 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. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4343 Number of models: 1 Model: "" Number of chains: 2 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: "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: 24 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 Restraints were copied for chains: P, C, B, E, D, G, F, I, H, K, J, M, L, O, N Time building chain proxies: 1.75, per 1000 atoms: 0.40 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 - 3.00 Amino acid : True - 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: 0.96 Conformation dependent library (CDL) restraints added in 511.5 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: 1.68 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: 1.05 Time building geometry restraints manager: 1.15 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: 0.00 - 1.42: 5162 1.42 - 2.83: 638 2.83 - 4.25: 240 4.25 - 5.67: 97 5.67 - 7.09: 23 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 3.120 nonbonded pdb=" O2' A P 11 " pdb=" NE2 HIS L 407 " model vdw 2.342 3.120 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 3.040 nonbonded pdb=" O SER G 422 " pdb=" OG SER G 422 " model vdw 2.483 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 0.120 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 407 TYR 0.008 0.002 TYR C 394 ARG 0.001 0.000 ARG I 406 *********************** 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 : 0.492 Fit side-chains REVERT: D 419 MET cc_start: 0.8199 (mtp) cc_final: 0.7993 (mtm) REVERT: G 406 ARG cc_start: 0.7065 (mtp85) cc_final: 0.6281 (mtm-85) REVERT: I 406 ARG cc_start: 0.6718 (mtp85) cc_final: 0.6404 (mtm180) REVERT: K 419 MET cc_start: 0.8060 (mtp) cc_final: 0.7753 (mtm) REVERT: N 406 ARG cc_start: 0.6509 (mtp85) cc_final: 0.5637 (mmt180) REVERT: O 406 ARG cc_start: 0.7051 (mtp85) cc_final: 0.5905 (mmt180) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1614 time to fit residues: 29.5770 Evaluate side-chains 108 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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: 0.7353 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4455 Z= 0.418 Angle : 0.887 6.749 6160 Z= 0.466 Chirality : 0.056 0.179 765 Planarity : 0.008 0.041 723 Dihedral : 21.675 123.870 767 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.84 % Allowed : 13.54 % Favored : 82.63 % 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: -2.78 (0.35), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 407 TYR 0.015 0.003 TYR G 394 ARG 0.005 0.001 ARG F 406 *********************** 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 138 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.454 Fit side-chains REVERT: C 406 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7845 (mtt90) REVERT: D 419 MET cc_start: 0.8655 (mtp) cc_final: 0.8210 (mtm) REVERT: G 406 ARG cc_start: 0.7776 (mtp85) cc_final: 0.6380 (mtm-85) REVERT: I 406 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6151 (mtm180) REVERT: K 419 MET cc_start: 0.8419 (mtp) cc_final: 0.7956 (mtm) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.1699 time to fit residues: 26.7688 Evaluate side-chains 107 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain K residue 409 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 407 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4455 Z= 0.249 Angle : 0.742 5.192 6160 Z= 0.386 Chirality : 0.049 0.173 765 Planarity : 0.006 0.037 723 Dihedral : 21.192 122.553 767 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.64 % Allowed : 16.97 % Favored : 79.39 % 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: -2.68 (0.35), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 407 TYR 0.010 0.002 TYR O 394 ARG 0.007 0.001 ARG D 406 *********************** 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 116 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.442 Fit side-chains REVERT: B 416 SER cc_start: 0.8032 (p) cc_final: 0.7831 (p) REVERT: D 406 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.7209 (mtt-85) REVERT: F 406 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7803 (mtt-85) REVERT: G 406 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6177 (mtm180) REVERT: H 406 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7181 (mtm-85) REVERT: I 406 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6075 (mtm180) REVERT: J 406 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7745 (mtt-85) REVERT: K 419 MET cc_start: 0.8320 (mtp) cc_final: 0.7979 (mtm) REVERT: N 406 ARG cc_start: 0.7001 (mtt-85) cc_final: 0.5232 (mmt180) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 0.1821 time to fit residues: 24.0617 Evaluate side-chains 108 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 406 ARG Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 416 SER 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: 7.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 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: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.034 4455 Z= 0.537 Angle : 0.933 7.298 6160 Z= 0.487 Chirality : 0.056 0.187 765 Planarity : 0.008 0.042 723 Dihedral : 21.530 123.961 767 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 5.05 % Allowed : 15.76 % Favored : 79.19 % 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: -3.18 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 407 TYR 0.020 0.003 TYR N 394 ARG 0.006 0.001 ARG L 406 *********************** 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 140 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.487 Fit side-chains REVERT: E 421 ASP cc_start: 0.8292 (t0) cc_final: 0.8058 (t0) REVERT: G 406 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6178 (mtm-85) REVERT: H 406 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7948 (mtm-85) REVERT: I 406 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6104 (mtm180) REVERT: K 419 MET cc_start: 0.8579 (mtp) cc_final: 0.8143 (mtm) REVERT: N 406 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.5539 (mmt180) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 0.1511 time to fit residues: 24.2112 Evaluate side-chains 127 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 406 ARG Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 416 SER Chi-restraints excluded: chain O residue 419 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4455 Z= 0.210 Angle : 0.735 5.763 6160 Z= 0.376 Chirality : 0.047 0.174 765 Planarity : 0.006 0.030 723 Dihedral : 20.892 121.526 767 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 5.05 % Allowed : 18.38 % Favored : 76.57 % 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: -2.99 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 407 TYR 0.010 0.002 TYR N 394 ARG 0.010 0.001 ARG D 406 *********************** 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 124 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.514 Fit side-chains REVERT: G 406 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6170 (mtm180) REVERT: I 406 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.5928 (mtm180) REVERT: N 406 ARG cc_start: 0.6983 (mtt-85) cc_final: 0.5376 (mmt180) REVERT: N 413 SER cc_start: 0.7738 (m) cc_final: 0.7322 (p) REVERT: N 421 ASP cc_start: 0.8461 (t0) cc_final: 0.8139 (t0) outliers start: 25 outliers final: 14 residues processed: 110 average time/residue: 0.1742 time to fit residues: 23.7675 Evaluate side-chains 107 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 416 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 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: 0.7290 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4455 Z= 0.245 Angle : 0.727 5.735 6160 Z= 0.374 Chirality : 0.049 0.176 765 Planarity : 0.006 0.033 723 Dihedral : 20.724 122.418 767 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.44 % Allowed : 18.79 % Favored : 76.77 % 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: -3.15 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 407 TYR 0.012 0.002 TYR N 394 ARG 0.007 0.001 ARG D 406 *********************** 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 124 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.502 Fit side-chains REVERT: G 406 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6181 (mtm180) REVERT: I 406 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5950 (mtm180) REVERT: N 406 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.5377 (mmt180) REVERT: N 413 SER cc_start: 0.7831 (m) cc_final: 0.7374 (p) REVERT: N 421 ASP cc_start: 0.8446 (t0) cc_final: 0.8119 (t0) outliers start: 22 outliers final: 16 residues processed: 113 average time/residue: 0.1722 time to fit residues: 24.2566 Evaluate side-chains 116 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 416 SER Chi-restraints excluded: chain O residue 419 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4455 Z= 0.288 Angle : 0.749 5.940 6160 Z= 0.388 Chirality : 0.050 0.180 765 Planarity : 0.006 0.032 723 Dihedral : 20.666 122.282 767 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.25 % Allowed : 18.79 % Favored : 75.96 % 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: -3.32 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 407 TYR 0.011 0.002 TYR N 394 ARG 0.005 0.001 ARG H 406 *********************** 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 124 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.506 Fit side-chains REVERT: G 406 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6178 (mtm180) REVERT: H 408 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7059 (mt) REVERT: I 406 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.5968 (mtm180) REVERT: N 406 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.5449 (mmt180) REVERT: N 413 SER cc_start: 0.7992 (m) cc_final: 0.7478 (p) REVERT: N 421 ASP cc_start: 0.8428 (t0) cc_final: 0.8069 (t0) outliers start: 26 outliers final: 20 residues processed: 109 average time/residue: 0.1537 time to fit residues: 21.1711 Evaluate side-chains 121 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 422 SER Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 404 SER Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 419 MET 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: 2.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4455 Z= 0.258 Angle : 0.723 5.864 6160 Z= 0.373 Chirality : 0.049 0.177 765 Planarity : 0.006 0.028 723 Dihedral : 20.484 121.561 767 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 4.24 % Allowed : 19.60 % Favored : 76.16 % 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: -3.38 (0.34), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 407 TYR 0.012 0.002 TYR N 394 ARG 0.007 0.001 ARG M 406 *********************** 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 120 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.492 Fit side-chains REVERT: G 406 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6246 (mtm180) REVERT: H 408 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7040 (mt) REVERT: I 406 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.5947 (mtm180) REVERT: K 406 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7596 (tpp-160) REVERT: N 406 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.5437 (mmt180) REVERT: N 413 SER cc_start: 0.8031 (m) cc_final: 0.7591 (p) REVERT: N 421 ASP cc_start: 0.8438 (t0) cc_final: 0.8083 (t0) outliers start: 21 outliers final: 18 residues processed: 106 average time/residue: 0.1761 time to fit residues: 23.1005 Evaluate side-chains 117 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain H residue 393 VAL Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 416 SER Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 419 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 0.0770 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 overall best weight: 7.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4455 Z= 0.418 Angle : 0.832 6.621 6160 Z= 0.433 Chirality : 0.054 0.195 765 Planarity : 0.007 0.041 723 Dihedral : 20.729 122.452 767 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Rotamer: Outliers : 5.25 % Allowed : 19.19 % Favored : 75.56 % 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: -3.64 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 407 TYR 0.017 0.002 TYR N 394 ARG 0.007 0.002 ARG M 406 *********************** 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 130 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.560 Fit side-chains REVERT: G 406 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6210 (mtm-85) REVERT: H 408 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7257 (mt) REVERT: I 406 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6097 (mtm180) REVERT: N 406 ARG cc_start: 0.7386 (mtt-85) cc_final: 0.5585 (mmt180) REVERT: N 421 ASP cc_start: 0.8425 (t0) cc_final: 0.8035 (t0) outliers start: 26 outliers final: 21 residues processed: 114 average time/residue: 0.1999 time to fit residues: 28.5870 Evaluate side-chains 126 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 422 SER Chi-restraints excluded: chain H residue 393 VAL Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 413 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4455 Z= 0.360 Angle : 0.803 6.235 6160 Z= 0.416 Chirality : 0.052 0.190 765 Planarity : 0.006 0.033 723 Dihedral : 20.668 122.780 767 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.10 % Favored : 84.90 % Rotamer: Outliers : 5.05 % Allowed : 19.19 % Favored : 75.76 % 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: -3.72 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 407 TYR 0.014 0.002 TYR N 394 ARG 0.007 0.002 ARG M 406 ********************** 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 130 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.447 Fit side-chains REVERT: G 406 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6158 (mtm-85) REVERT: H 408 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7193 (mt) REVERT: I 406 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6029 (mtm180) REVERT: N 406 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.5476 (mmt180) REVERT: N 421 ASP cc_start: 0.8434 (t0) cc_final: 0.8033 (t0) outliers start: 25 outliers final: 20 residues processed: 114 average time/residue: 0.1618 time to fit residues: 23.3083 Evaluate side-chains 127 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 406 ARG Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain G residue 422 SER Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 406 ARG Chi-restraints excluded: chain I residue 422 SER Chi-restraints excluded: chain J residue 404 SER Chi-restraints excluded: chain J residue 419 MET Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 419 MET Chi-restraints excluded: chain M residue 404 SER Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain O residue 414 THR Chi-restraints excluded: chain O residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.232549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.192795 restraints weight = 4300.498| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 2.40 r_work: 0.4885 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4455 Z= 0.325 Angle : 0.776 6.055 6160 Z= 0.401 Chirality : 0.051 0.190 765 Planarity : 0.006 0.031 723 Dihedral : 20.526 122.538 767 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.27 % Favored : 83.73 % Rotamer: Outliers : 5.45 % Allowed : 18.59 % Favored : 75.96 % 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: -3.77 (0.33), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 407 TYR 0.014 0.002 TYR N 394 ARG 0.007 0.001 ARG F 406 =============================================================================== Job complete usr+sys time: 1133.37 seconds wall clock time: 21 minutes 9.06 seconds (1269.06 seconds total)