Starting phenix.real_space_refine on Tue Feb 11 02:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.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/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.map" model { file = "/net/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gbr_29920/02_2025/8gbr_29920.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2345 2.51 5 N 600 2.21 5 O 680 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-5592/modules/chem_data/mon_lib" Total number of atoms: 3630 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.08, per 1000 atoms: 0.57 Number of scatterers: 3630 At special positions: 0 Unit cell: (87.978, 70.004, 42.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 680 8.00 N 600 7.00 C 2345 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: 0.82 Conformation dependent library (CDL) restraints added in 418.9 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 880 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 51.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.395A pdb=" N VAL A 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20 removed outlier: 6.600A pdb=" N ALA B 19 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 34 removed outlier: 6.593A pdb=" N ALA B 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL D 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN B 27 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL D 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 29 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL D 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ARG D 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 33 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL B 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN A 27 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 29 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG B 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 33 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.847A pdb=" N PHE B 64 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 65 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 66 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 65 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLU C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU A 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLU A 63 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N GLU C 66 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N VAL A 65 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR C 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU E 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE E 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU C 63 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLU E 66 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL C 65 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.577A pdb=" N LYS A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE C 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE E 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU C 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80 removed outlier: 7.015A pdb=" N SER B 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N LYS C 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N TRP E 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99 removed outlier: 6.810A pdb=" N VAL B 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR D 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE B 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN D 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA B 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110 removed outlier: 6.532A pdb=" N ARG B 103 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR D 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR B 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA D 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ILE B 107 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU D 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ALA B 109 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 103 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR B 106 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA B 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE A 107 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 110 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA C 109 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA E 109 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU C 110 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115 removed outlier: 7.054A pdb=" N TYR A 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR C 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123 removed outlier: 5.845A pdb=" N THR B 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL D 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR D 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL B 122 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR B 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 122 " --> pdb=" O THR B 123 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1140 1.34 - 1.45: 496 1.45 - 1.57: 2069 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 3715 Sorted by residual: bond pdb=" C MET B 13 " pdb=" O MET B 13 " ideal model delta sigma weight residual 1.236 1.222 0.013 1.20e-02 6.94e+03 1.24e+00 bond pdb=" C MET A 13 " pdb=" O MET A 13 " ideal model delta sigma weight residual 1.236 1.222 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" C MET C 13 " pdb=" O MET C 13 " ideal model delta sigma weight residual 1.236 1.222 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" C MET D 13 " pdb=" O MET D 13 " ideal model delta sigma weight residual 1.236 1.222 0.013 1.20e-02 6.94e+03 1.22e+00 bond pdb=" C MET E 13 " pdb=" O MET E 13 " ideal model delta sigma weight residual 1.236 1.223 0.012 1.20e-02 6.94e+03 1.06e+00 ... (remaining 3710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.76: 4370 0.76 - 1.52: 545 1.52 - 2.28: 76 2.28 - 3.04: 34 3.04 - 3.80: 30 Bond angle restraints: 5055 Sorted by residual: angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 117.20 -3.30 1.80e+00 3.09e-01 3.36e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 117.17 -3.27 1.80e+00 3.09e-01 3.31e+00 angle pdb=" CA TYR D 114 " pdb=" CB TYR D 114 " pdb=" CG TYR D 114 " ideal model delta sigma weight residual 113.90 117.17 -3.27 1.80e+00 3.09e-01 3.30e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 117.15 -3.25 1.80e+00 3.09e-01 3.27e+00 angle pdb=" CA TYR E 114 " pdb=" CB TYR E 114 " pdb=" CG TYR E 114 " ideal model delta sigma weight residual 113.90 117.13 -3.23 1.80e+00 3.09e-01 3.23e+00 ... (remaining 5050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 1955 15.69 - 31.37: 185 31.37 - 47.06: 35 47.06 - 62.75: 5 62.75 - 78.43: 10 Dihedral angle restraints: 2190 sinusoidal: 830 harmonic: 1360 Sorted by residual: dihedral pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " pdb=" CZ ARG B 34 " ideal model delta sinusoidal sigma weight residual 90.00 41.41 48.59 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " ideal model delta sinusoidal sigma weight residual 90.00 41.46 48.54 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " pdb=" CZ ARG A 34 " ideal model delta sinusoidal sigma weight residual 90.00 41.47 48.53 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 2187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 260 0.026 - 0.052: 193 0.052 - 0.078: 53 0.078 - 0.104: 42 0.104 - 0.129: 47 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA VAL E 121 " pdb=" N VAL E 121 " pdb=" C VAL E 121 " pdb=" CB VAL E 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL A 65 " pdb=" N VAL A 65 " pdb=" C VAL A 65 " pdb=" CB VAL A 65 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 592 not shown) Planarity restraints: 625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 23 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO D 24 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 24 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 24 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 23 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO C 24 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 23 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 24 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " 0.029 5.00e-02 4.00e+02 ... (remaining 622 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 30 2.68 - 3.23: 3036 3.23 - 3.79: 5151 3.79 - 4.34: 7288 4.34 - 4.90: 12102 Nonbonded interactions: 27607 Sorted by model distance: nonbonded pdb=" OG SER A 112 " pdb=" O SER B 112 " model vdw 2.120 3.040 nonbonded pdb=" O SER A 112 " pdb=" OG SER C 112 " model vdw 2.128 3.040 nonbonded pdb=" OG SER B 112 " pdb=" O SER D 112 " model vdw 2.148 3.040 nonbonded pdb=" O SER C 112 " pdb=" OG SER E 112 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR B 114 " model vdw 2.585 3.040 ... (remaining 27602 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.480 Find NCS groups from input model: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.004 0.039 3715 Z= 0.270 Angle : 0.593 3.796 5055 Z= 0.343 Chirality : 0.050 0.129 595 Planarity : 0.007 0.053 625 Dihedral : 13.841 78.434 1310 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % 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: -2.35 (0.38), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.001 0.000 HIS D 31 PHE 0.008 0.002 PHE B 87 TYR 0.016 0.002 TYR E 114 ARG 0.009 0.002 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.323 Fit side-chains REVERT: A 70 LYS cc_start: 0.8728 (tttt) cc_final: 0.8487 (tttt) REVERT: A 85 SER cc_start: 0.9353 (m) cc_final: 0.9115 (t) REVERT: D 70 LYS cc_start: 0.8905 (tttt) cc_final: 0.8376 (tppt) REVERT: E 34 ARG cc_start: 0.8448 (ttt90) cc_final: 0.7335 (pmt-80) REVERT: E 76 LYS cc_start: 0.8802 (mttp) cc_final: 0.8438 (mmmt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1937 time to fit residues: 36.4206 Evaluate side-chains 120 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 0.0470 chunk 18 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086167 restraints weight = 9241.523| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.70 r_work: 0.3613 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3715 Z= 0.337 Angle : 0.654 5.757 5055 Z= 0.340 Chirality : 0.049 0.136 595 Planarity : 0.005 0.040 625 Dihedral : 4.777 13.317 500 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.28 % Allowed : 16.71 % Favored : 81.01 % 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: -2.37 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.001 0.000 HIS E 90 PHE 0.019 0.002 PHE D 33 TYR 0.014 0.002 TYR C 69 ARG 0.007 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.400 Fit side-chains REVERT: A 33 PHE cc_start: 0.8810 (t80) cc_final: 0.8527 (t80) REVERT: A 85 SER cc_start: 0.9041 (m) cc_final: 0.8446 (t) REVERT: B 12 LEU cc_start: 0.9335 (tt) cc_final: 0.9129 (tt) REVERT: B 69 TYR cc_start: 0.9109 (m-80) cc_final: 0.8889 (m-80) REVERT: B 76 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8834 (mttm) REVERT: B 99 ASP cc_start: 0.8369 (t0) cc_final: 0.8153 (t0) REVERT: C 13 MET cc_start: 0.8307 (mtp) cc_final: 0.7871 (ttm) REVERT: C 69 TYR cc_start: 0.9200 (m-80) cc_final: 0.8817 (m-80) REVERT: C 89 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8679 (mp0) REVERT: D 70 LYS cc_start: 0.8637 (tttt) cc_final: 0.7803 (tppt) REVERT: D 72 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8415 (mt-10) REVERT: D 76 LYS cc_start: 0.9225 (mttp) cc_final: 0.8873 (mttm) REVERT: E 34 ARG cc_start: 0.8973 (ttt90) cc_final: 0.7130 (pmt-80) REVERT: E 72 GLU cc_start: 0.4542 (pm20) cc_final: 0.3878 (pm20) REVERT: E 76 LYS cc_start: 0.8610 (mttp) cc_final: 0.7528 (mmmt) outliers start: 9 outliers final: 8 residues processed: 134 average time/residue: 0.1720 time to fit residues: 27.7145 Evaluate side-chains 134 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.088240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.079172 restraints weight = 9411.727| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.81 r_work: 0.3616 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3715 Z= 0.256 Angle : 0.596 5.764 5055 Z= 0.311 Chirality : 0.048 0.132 595 Planarity : 0.004 0.028 625 Dihedral : 4.541 13.242 500 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.29 % Allowed : 15.95 % Favored : 80.76 % 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: -2.48 (0.36), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.001 0.000 HIS C 88 PHE 0.013 0.002 PHE D 33 TYR 0.012 0.001 TYR C 69 ARG 0.006 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.420 Fit side-chains REVERT: A 76 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8811 (mttp) REVERT: A 85 SER cc_start: 0.9001 (m) cc_final: 0.8373 (t) REVERT: B 69 TYR cc_start: 0.9063 (m-80) cc_final: 0.8799 (m-80) REVERT: B 99 ASP cc_start: 0.8498 (t0) cc_final: 0.8157 (t0) REVERT: C 13 MET cc_start: 0.8529 (mtp) cc_final: 0.7865 (ttm) REVERT: C 69 TYR cc_start: 0.9161 (m-80) cc_final: 0.8792 (m-80) REVERT: C 89 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8652 (mp0) REVERT: D 70 LYS cc_start: 0.8523 (tttt) cc_final: 0.7778 (tppt) REVERT: D 72 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 76 LYS cc_start: 0.9194 (mttp) cc_final: 0.8894 (mttm) REVERT: D 92 GLU cc_start: 0.7298 (mp0) cc_final: 0.7026 (mp0) REVERT: E 34 ARG cc_start: 0.8917 (ttt90) cc_final: 0.7020 (pmt-80) REVERT: E 76 LYS cc_start: 0.8478 (mttp) cc_final: 0.7666 (mmmt) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.1695 time to fit residues: 27.7554 Evaluate side-chains 135 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.099727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.086533 restraints weight = 9789.698| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.89 r_work: 0.3595 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3715 Z= 0.420 Angle : 0.651 5.321 5055 Z= 0.344 Chirality : 0.048 0.134 595 Planarity : 0.004 0.023 625 Dihedral : 4.619 14.489 500 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.81 % Allowed : 15.19 % Favored : 80.00 % 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: -2.53 (0.36), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS D 88 PHE 0.014 0.002 PHE A 95 TYR 0.015 0.002 TYR C 69 ARG 0.005 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.438 Fit side-chains REVERT: A 76 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8942 (mttm) REVERT: B 69 TYR cc_start: 0.9138 (m-80) cc_final: 0.8887 (m-80) REVERT: B 89 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8870 (mp0) REVERT: B 99 ASP cc_start: 0.8572 (t0) cc_final: 0.8187 (t0) REVERT: C 13 MET cc_start: 0.8662 (mtp) cc_final: 0.8035 (ttm) REVERT: C 62 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: C 69 TYR cc_start: 0.9285 (m-80) cc_final: 0.8983 (m-80) REVERT: C 89 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8687 (mp0) REVERT: D 76 LYS cc_start: 0.9261 (mttp) cc_final: 0.8951 (mttm) REVERT: D 92 GLU cc_start: 0.7497 (mp0) cc_final: 0.7171 (mp0) REVERT: E 34 ARG cc_start: 0.8837 (ttt90) cc_final: 0.7037 (pmt-80) REVERT: E 76 LYS cc_start: 0.8649 (mttp) cc_final: 0.7891 (mmmt) REVERT: E 92 GLU cc_start: 0.4367 (pm20) cc_final: 0.4040 (pm20) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.1449 time to fit residues: 22.8831 Evaluate side-chains 135 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089401 restraints weight = 9202.845| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.79 r_work: 0.3651 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3715 Z= 0.362 Angle : 0.639 5.540 5055 Z= 0.333 Chirality : 0.048 0.129 595 Planarity : 0.003 0.021 625 Dihedral : 4.637 14.364 500 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.81 % Allowed : 15.44 % Favored : 79.75 % 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: -2.56 (0.36), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS C 88 PHE 0.012 0.002 PHE D 33 TYR 0.015 0.002 TYR C 69 ARG 0.004 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.476 Fit side-chains REVERT: A 76 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8890 (mttm) REVERT: B 69 TYR cc_start: 0.9135 (m-80) cc_final: 0.8895 (m-80) REVERT: B 89 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8893 (mp0) REVERT: B 99 ASP cc_start: 0.8572 (t0) cc_final: 0.8186 (t0) REVERT: C 13 MET cc_start: 0.8662 (mtp) cc_final: 0.7852 (ttm) REVERT: C 62 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: C 69 TYR cc_start: 0.9253 (m-80) cc_final: 0.8964 (m-80) REVERT: C 89 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8703 (mp0) REVERT: D 76 LYS cc_start: 0.9291 (mttp) cc_final: 0.8987 (mttm) REVERT: E 34 ARG cc_start: 0.8829 (ttt90) cc_final: 0.7081 (pmt-80) REVERT: E 58 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6629 (mt) REVERT: E 76 LYS cc_start: 0.8545 (mttp) cc_final: 0.7948 (mmmt) REVERT: E 92 GLU cc_start: 0.4242 (pm20) cc_final: 0.3833 (pm20) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.1425 time to fit residues: 22.0743 Evaluate side-chains 135 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.093763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082261 restraints weight = 9543.548| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.89 r_work: 0.3557 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3715 Z= 0.405 Angle : 0.680 6.714 5055 Z= 0.349 Chirality : 0.048 0.131 595 Planarity : 0.003 0.021 625 Dihedral : 4.653 15.063 500 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.30 % Allowed : 14.94 % Favored : 80.76 % 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: -2.69 (0.36), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS D 88 PHE 0.012 0.002 PHE B 33 TYR 0.015 0.002 TYR C 69 ARG 0.003 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.472 Fit side-chains REVERT: A 76 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8661 (mttm) REVERT: B 89 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8762 (mp0) REVERT: B 99 ASP cc_start: 0.8389 (t0) cc_final: 0.8033 (t0) REVERT: C 13 MET cc_start: 0.8564 (mtp) cc_final: 0.7792 (ttm) REVERT: C 62 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: C 69 TYR cc_start: 0.9051 (m-80) cc_final: 0.8646 (m-80) REVERT: C 89 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8676 (mp0) REVERT: D 76 LYS cc_start: 0.9136 (mttp) cc_final: 0.8798 (mttm) REVERT: E 34 ARG cc_start: 0.8681 (ttt90) cc_final: 0.6946 (pmt-80) REVERT: E 76 LYS cc_start: 0.8038 (mttp) cc_final: 0.7772 (mmmt) REVERT: E 92 GLU cc_start: 0.4071 (pm20) cc_final: 0.3671 (pm20) outliers start: 17 outliers final: 16 residues processed: 122 average time/residue: 0.1384 time to fit residues: 21.0970 Evaluate side-chains 133 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.101632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.088579 restraints weight = 9341.268| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.95 r_work: 0.3608 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3715 Z= 0.318 Angle : 0.663 7.199 5055 Z= 0.341 Chirality : 0.048 0.129 595 Planarity : 0.003 0.023 625 Dihedral : 4.635 15.481 500 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.80 % Allowed : 15.70 % Favored : 80.51 % 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: -2.70 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 79 HIS 0.002 0.001 HIS C 88 PHE 0.013 0.002 PHE C 33 TYR 0.013 0.001 TYR B 69 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.413 Fit side-chains REVERT: A 76 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8670 (mttm) REVERT: B 89 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8799 (mp0) REVERT: B 99 ASP cc_start: 0.8440 (t0) cc_final: 0.8063 (t0) REVERT: C 13 MET cc_start: 0.8607 (mtp) cc_final: 0.7816 (ttm) REVERT: C 62 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: C 69 TYR cc_start: 0.8923 (m-80) cc_final: 0.8586 (m-80) REVERT: C 89 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8665 (mp0) REVERT: D 70 LYS cc_start: 0.8462 (tttt) cc_final: 0.7692 (tppt) REVERT: D 76 LYS cc_start: 0.9171 (mttp) cc_final: 0.8812 (mttm) REVERT: E 34 ARG cc_start: 0.8707 (ttt90) cc_final: 0.6959 (pmt-80) REVERT: E 58 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.5868 (mt) REVERT: E 76 LYS cc_start: 0.8111 (mttp) cc_final: 0.7905 (mmmt) REVERT: E 92 GLU cc_start: 0.4260 (pm20) cc_final: 0.3843 (pm20) outliers start: 15 outliers final: 13 residues processed: 126 average time/residue: 0.1404 time to fit residues: 21.9318 Evaluate side-chains 133 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 0.0770 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.100273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087275 restraints weight = 9132.732| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.85 r_work: 0.3573 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3715 Z= 0.343 Angle : 0.682 6.838 5055 Z= 0.348 Chirality : 0.047 0.139 595 Planarity : 0.003 0.020 625 Dihedral : 4.618 15.431 500 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 5.06 % Allowed : 15.44 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 79 HIS 0.002 0.001 HIS D 88 PHE 0.011 0.001 PHE B 33 TYR 0.012 0.001 TYR B 69 ARG 0.003 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.360 Fit side-chains REVERT: A 76 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8670 (mttm) REVERT: B 89 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8805 (mp0) REVERT: B 99 ASP cc_start: 0.8354 (t0) cc_final: 0.7993 (t0) REVERT: C 13 MET cc_start: 0.8613 (mtp) cc_final: 0.7835 (ttm) REVERT: C 62 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7833 (tp30) REVERT: C 69 TYR cc_start: 0.8919 (m-80) cc_final: 0.8520 (m-80) REVERT: C 89 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8687 (mp0) REVERT: D 70 LYS cc_start: 0.8424 (tttt) cc_final: 0.7667 (tppt) REVERT: D 76 LYS cc_start: 0.9175 (mttp) cc_final: 0.8801 (mttm) REVERT: E 34 ARG cc_start: 0.8694 (ttt90) cc_final: 0.6944 (pmt-80) REVERT: E 58 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5830 (mt) REVERT: E 92 GLU cc_start: 0.4060 (pm20) cc_final: 0.3684 (pm20) outliers start: 20 outliers final: 18 residues processed: 123 average time/residue: 0.1380 time to fit residues: 21.0447 Evaluate side-chains 137 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.103278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.090301 restraints weight = 9208.041| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.89 r_work: 0.3611 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3715 Z= 0.276 Angle : 0.694 7.376 5055 Z= 0.351 Chirality : 0.048 0.138 595 Planarity : 0.003 0.021 625 Dihedral : 4.572 15.603 500 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.30 % Allowed : 16.71 % Favored : 78.99 % 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: -2.71 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 79 HIS 0.003 0.001 HIS A 31 PHE 0.013 0.001 PHE C 33 TYR 0.012 0.001 TYR B 69 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.413 Fit side-chains REVERT: A 59 THR cc_start: 0.8790 (m) cc_final: 0.8406 (p) REVERT: A 76 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8769 (mttm) REVERT: B 89 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8817 (mp0) REVERT: B 99 ASP cc_start: 0.8438 (t0) cc_final: 0.7958 (t0) REVERT: C 13 MET cc_start: 0.8648 (mtp) cc_final: 0.7893 (ttm) REVERT: C 62 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: C 69 TYR cc_start: 0.8929 (m-80) cc_final: 0.8541 (m-80) REVERT: C 89 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8697 (mp0) REVERT: D 70 LYS cc_start: 0.8616 (tttt) cc_final: 0.7801 (tppt) REVERT: D 76 LYS cc_start: 0.9215 (mttp) cc_final: 0.8853 (mttm) REVERT: E 34 ARG cc_start: 0.8764 (ttt90) cc_final: 0.7043 (pmt-80) REVERT: E 58 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5891 (mt) REVERT: E 92 GLU cc_start: 0.4110 (pm20) cc_final: 0.3736 (pm20) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.1401 time to fit residues: 21.2942 Evaluate side-chains 133 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.098949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.086979 restraints weight = 9416.681| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.93 r_work: 0.3618 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3715 Z= 0.270 Angle : 0.701 7.736 5055 Z= 0.353 Chirality : 0.048 0.136 595 Planarity : 0.003 0.020 625 Dihedral : 4.499 14.868 500 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.80 % Allowed : 17.47 % Favored : 78.73 % 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: -2.71 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 79 HIS 0.003 0.001 HIS A 31 PHE 0.020 0.001 PHE D 33 TYR 0.011 0.001 TYR B 69 ARG 0.003 0.001 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.385 Fit side-chains REVERT: A 28 VAL cc_start: 0.9306 (t) cc_final: 0.9030 (m) REVERT: A 59 THR cc_start: 0.8779 (m) cc_final: 0.8455 (p) REVERT: A 76 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8767 (mttm) REVERT: B 89 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8815 (mp0) REVERT: B 99 ASP cc_start: 0.8247 (t0) cc_final: 0.8045 (t0) REVERT: C 13 MET cc_start: 0.8617 (mtp) cc_final: 0.7845 (ttm) REVERT: C 62 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: C 69 TYR cc_start: 0.8908 (m-80) cc_final: 0.8499 (m-80) REVERT: C 89 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8674 (mp0) REVERT: D 70 LYS cc_start: 0.8498 (tttt) cc_final: 0.7711 (tppt) REVERT: D 74 ASP cc_start: 0.9083 (t0) cc_final: 0.8784 (t0) REVERT: D 76 LYS cc_start: 0.9196 (mttp) cc_final: 0.8864 (mttm) REVERT: D 92 GLU cc_start: 0.8043 (mp0) cc_final: 0.7756 (mp0) REVERT: E 34 ARG cc_start: 0.8745 (ttt90) cc_final: 0.7020 (pmt-80) REVERT: E 58 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5857 (mt) REVERT: E 92 GLU cc_start: 0.4087 (pm20) cc_final: 0.3712 (pm20) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.1334 time to fit residues: 20.7429 Evaluate side-chains 136 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.098623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.086947 restraints weight = 9402.661| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.86 r_work: 0.3609 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3715 Z= 0.332 Angle : 0.706 7.139 5055 Z= 0.359 Chirality : 0.048 0.134 595 Planarity : 0.003 0.019 625 Dihedral : 4.610 16.106 500 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.81 % Allowed : 16.71 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.37), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 79 HIS 0.002 0.001 HIS A 31 PHE 0.020 0.002 PHE D 33 TYR 0.010 0.001 TYR B 69 ARG 0.003 0.001 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.89 seconds wall clock time: 31 minutes 58.59 seconds (1918.59 seconds total)