Starting phenix.real_space_refine on Sun Mar 10 22:42:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/03_2024/7vo9_32049_neut.pdb" } resolution = 3.8 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= 0.002 sd= 0.043 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 86 5.49 5 S 24 5.16 5 C 3247 2.51 5 N 1066 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 27": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5711 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2419 SG CYS G 90 17.241 31.300 59.728 1.00 71.88 S ATOM 2441 SG CYS G 93 14.793 30.618 62.671 1.00 70.47 S ATOM 2714 SG CYS G 130 14.935 28.682 59.367 1.00 73.41 S ATOM 2733 SG CYS G 133 13.753 32.726 60.427 1.00 76.67 S ATOM 2333 SG CYS G 79 25.843 20.667 68.382 1.00 55.29 S ATOM 3403 SG CYS H 90 50.589 21.848 55.123 1.00 65.50 S ATOM 3425 SG CYS H 93 53.560 23.049 52.848 1.00 67.51 S ATOM 3698 SG CYS H 130 51.610 19.758 52.799 1.00 70.00 S ATOM 3717 SG CYS H 133 54.743 21.183 55.225 1.00 77.21 S ATOM 3317 SG CYS H 79 41.604 31.101 44.386 1.00 60.89 S ATOM 4387 SG CYS M 90 18.888 56.432 98.247 1.00 65.11 S ATOM 4409 SG CYS M 93 16.467 57.794 95.462 1.00 65.03 S ATOM 4682 SG CYS M 130 15.148 58.615 98.647 1.00 66.03 S ATOM 4701 SG CYS M 133 15.423 55.317 97.309 1.00 76.02 S ATOM 4301 SG CYS M 79 28.244 66.312 88.717 1.00 55.78 S ATOM 5371 SG CYS N 90 52.577 62.137 102.734 1.00 63.37 S ATOM 5393 SG CYS N 93 56.120 61.109 103.694 1.00 66.66 S ATOM 5666 SG CYS N 130 54.023 63.902 105.638 1.00 70.51 S ATOM 5285 SG CYS N 79 41.722 54.410 113.951 1.00 42.33 S Time building chain proxies: 3.80, per 1000 atoms: 0.67 Number of scatterers: 5711 At special positions: 0 Unit cell: (73.7, 90.2, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 24 16.00 P 86 15.00 O 1276 8.00 N 1066 7.00 C 3247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 923.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " Number of angles added : 18 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 48.9% alpha, 17.9% beta 31 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'G' and resid 13 through 26 Processing helix chain 'G' and resid 31 through 43 Processing helix chain 'G' and resid 47 through 62 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.724A pdb=" N GLU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 116 removed outlier: 3.882A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'M' and resid 13 through 26 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 3.614A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 Processing sheet with id=AA1, first strand: chain 'G' and resid 65 through 68 Processing sheet with id=AA2, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.678A pdb=" N LYS G 95 " --> pdb=" O CYS G 90 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR G 117 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS H 130 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN G 119 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY H 128 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA G 121 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE H 126 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR G 123 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL H 124 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU G 125 " --> pdb=" O HIS H 122 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N HIS H 122 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE G 127 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL H 120 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR G 129 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AA5, first strand: chain 'M' and resid 64 through 68 Processing sheet with id=AA6, first strand: chain 'M' and resid 96 through 99 removed outlier: 6.098A pdb=" N HIS M 87 " --> pdb=" O ILE M 126 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY M 128 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL M 89 " --> pdb=" O GLY M 128 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN N 119 " --> pdb=" O THR M 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AA8, first strand: chain 'N' and resid 95 through 99 220 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 2.77 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: 1007 1.33 - 1.45: 1909 1.45 - 1.58: 2866 1.58 - 1.70: 170 1.70 - 1.82: 28 Bond restraints: 5980 Sorted by residual: bond pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.32e+01 bond pdb=" N VAL M 89 " pdb=" CA VAL M 89 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N ILE N 126 " pdb=" CA ILE N 126 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N VAL M 64 " pdb=" CA VAL M 64 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N VAL N 64 " pdb=" CA VAL N 64 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.22e-02 6.72e+03 1.09e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.46: 767 107.46 - 114.20: 3203 114.20 - 120.93: 2515 120.93 - 127.67: 1815 127.67 - 134.40: 165 Bond angle restraints: 8465 Sorted by residual: angle pdb=" C4' DT A 33 " pdb=" C3' DT A 33 " pdb=" O3' DT A 33 " ideal model delta sigma weight residual 110.00 118.05 -8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" O3' DT B 82 " pdb=" C3' DT B 82 " pdb=" C2' DT B 82 " ideal model delta sigma weight residual 111.50 119.05 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CA HIS M 86 " pdb=" CB HIS M 86 " pdb=" CG HIS M 86 " ideal model delta sigma weight residual 113.80 109.06 4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" N GLY G 94 " pdb=" CA GLY G 94 " pdb=" C GLY G 94 " ideal model delta sigma weight residual 115.30 108.81 6.49 1.39e+00 5.18e-01 2.18e+01 angle pdb=" N GLY M 94 " pdb=" CA GLY M 94 " pdb=" C GLY M 94 " ideal model delta sigma weight residual 115.36 109.19 6.17 1.33e+00 5.65e-01 2.15e+01 ... (remaining 8460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 3015 35.05 - 70.09: 280 70.09 - 105.13: 2 105.13 - 140.18: 7 140.18 - 175.22: 6 Dihedral angle restraints: 3310 sinusoidal: 1818 harmonic: 1492 Sorted by residual: dihedral pdb=" C ASP N 60 " pdb=" N ASP N 60 " pdb=" CA ASP N 60 " pdb=" CB ASP N 60 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C4' DG A 11 " pdb=" C3' DG A 11 " pdb=" O3' DG A 11 " pdb=" P DA A 12 " ideal model delta sinusoidal sigma weight residual -140.00 35.22 -175.22 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC A 1 " pdb=" C3' DC A 1 " pdb=" O3' DC A 1 " pdb=" P DA A 2 " ideal model delta sinusoidal sigma weight residual 220.00 46.22 173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 3307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 645 0.083 - 0.165: 255 0.165 - 0.248: 50 0.248 - 0.330: 3 0.330 - 0.412: 3 Chirality restraints: 956 Sorted by residual: chirality pdb=" C3' DT B 82 " pdb=" C4' DT B 82 " pdb=" O3' DT B 82 " pdb=" C2' DT B 82 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C3' DG B 56 " pdb=" C4' DG B 56 " pdb=" O3' DG B 56 " pdb=" C2' DG B 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ASP N 60 " pdb=" N ASP N 60 " pdb=" C ASP N 60 " pdb=" CB ASP N 60 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 953 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 122 " 0.011 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG HIS G 122 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS G 122 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS G 122 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS G 122 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS G 122 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS M 86 " -0.019 2.00e-02 2.50e+03 1.93e-02 5.56e+00 pdb=" CG HIS M 86 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS M 86 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 72 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C GLY M 72 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY M 72 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU M 73 " 0.012 2.00e-02 2.50e+03 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 179 2.68 - 3.23: 4633 3.23 - 3.79: 10248 3.79 - 4.34: 13092 4.34 - 4.90: 18444 Nonbonded interactions: 46596 Sorted by model distance: nonbonded pdb=" OD2 ASP H 65 " pdb="ZN ZN H 202 " model vdw 2.124 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.230 2.230 nonbonded pdb=" C2' DG B 42 " pdb=" O5' DT B 43 " model vdw 2.332 3.440 nonbonded pdb=" C2' DT B 71 " pdb=" N7 DG B 72 " model vdw 2.439 3.520 nonbonded pdb=" O ILE M 111 " pdb=" ND1 HIS M 115 " model vdw 2.496 2.520 ... (remaining 46591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.120 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: 5.540 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 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 : 0.011 0.044 5980 Z= 0.732 Angle : 1.580 8.054 8465 Z= 1.205 Chirality : 0.088 0.412 956 Planarity : 0.004 0.027 802 Dihedral : 23.203 175.224 2350 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.76 % Allowed : 10.61 % Favored : 88.64 % Cbeta Deviations : 0.21 % 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: 2.89 (0.34), residues: 516 helix: 3.25 (0.28), residues: 256 sheet: 0.71 (0.51), residues: 88 loop : 0.54 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 107 HIS 0.040 0.003 HIS G 122 PHE 0.014 0.003 PHE G 29 TYR 0.016 0.003 TYR G 117 ARG 0.005 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 111 ILE cc_start: 0.7594 (pt) cc_final: 0.6963 (pt) REVERT: N 52 TYR cc_start: 0.7282 (m-80) cc_final: 0.6971 (m-80) REVERT: N 99 VAL cc_start: 0.8508 (m) cc_final: 0.8074 (t) outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.3144 time to fit residues: 58.9422 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 HIS M 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5980 Z= 0.289 Angle : 0.713 7.927 8465 Z= 0.417 Chirality : 0.042 0.147 956 Planarity : 0.005 0.045 802 Dihedral : 27.517 179.104 1494 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.29 % Allowed : 21.21 % Favored : 74.49 % 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: 2.31 (0.34), residues: 516 helix: 2.80 (0.29), residues: 256 sheet: 0.30 (0.46), residues: 104 loop : 0.32 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 107 HIS 0.008 0.002 HIS N 86 PHE 0.018 0.002 PHE G 127 TYR 0.010 0.002 TYR H 117 ARG 0.004 0.001 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7983 (p) REVERT: M 126 ILE cc_start: 0.8164 (tp) cc_final: 0.7947 (pt) REVERT: N 11 ARG cc_start: 0.6014 (mmp80) cc_final: 0.5668 (mmp80) outliers start: 17 outliers final: 8 residues processed: 95 average time/residue: 0.2587 time to fit residues: 29.8036 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 84 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5980 Z= 0.267 Angle : 0.667 9.031 8465 Z= 0.383 Chirality : 0.041 0.151 956 Planarity : 0.004 0.029 802 Dihedral : 28.670 176.585 1494 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.81 % Allowed : 22.22 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.35), residues: 516 helix: 2.49 (0.30), residues: 256 sheet: 0.05 (0.46), residues: 104 loop : 0.31 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP M 107 HIS 0.007 0.002 HIS N 86 PHE 0.018 0.002 PHE G 127 TYR 0.015 0.002 TYR N 117 ARG 0.004 0.001 ARG N 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.5606 (m90) REVERT: M 126 ILE cc_start: 0.8401 (tp) cc_final: 0.8091 (pt) REVERT: N 11 ARG cc_start: 0.6427 (mmp80) cc_final: 0.6138 (mmp80) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.2576 time to fit residues: 26.8961 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5980 Z= 0.260 Angle : 0.676 10.342 8465 Z= 0.383 Chirality : 0.041 0.194 956 Planarity : 0.004 0.027 802 Dihedral : 28.910 178.371 1494 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 7.58 % Allowed : 22.98 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.35), residues: 516 helix: 2.26 (0.31), residues: 256 sheet: -0.10 (0.47), residues: 104 loop : 0.23 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP M 107 HIS 0.006 0.001 HIS N 86 PHE 0.016 0.002 PHE G 127 TYR 0.010 0.002 TYR N 76 ARG 0.010 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6885 (tp-100) REVERT: G 87 HIS cc_start: 0.5841 (OUTLIER) cc_final: 0.5338 (m90) REVERT: M 51 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7031 (p) REVERT: M 104 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (p) REVERT: M 126 ILE cc_start: 0.8386 (tp) cc_final: 0.8115 (pt) REVERT: N 11 ARG cc_start: 0.6663 (mmp80) cc_final: 0.6420 (mmp80) REVERT: N 14 ARG cc_start: 0.5590 (ttp80) cc_final: 0.5077 (tmm160) outliers start: 30 outliers final: 19 residues processed: 87 average time/residue: 0.2297 time to fit residues: 24.5734 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5980 Z= 0.287 Angle : 0.679 10.750 8465 Z= 0.385 Chirality : 0.041 0.152 956 Planarity : 0.004 0.039 802 Dihedral : 29.406 177.247 1494 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 7.83 % Allowed : 22.98 % Favored : 69.19 % 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: 1.41 (0.35), residues: 516 helix: 1.95 (0.30), residues: 256 sheet: -0.33 (0.46), residues: 104 loop : 0.30 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP M 107 HIS 0.007 0.001 HIS N 86 PHE 0.017 0.002 PHE G 127 TYR 0.013 0.002 TYR N 117 ARG 0.004 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6964 (tp-100) REVERT: G 87 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5300 (m90) REVERT: M 51 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7112 (p) REVERT: M 104 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8236 (p) REVERT: N 14 ARG cc_start: 0.5780 (ttp80) cc_final: 0.5275 (tmm160) outliers start: 31 outliers final: 21 residues processed: 89 average time/residue: 0.2097 time to fit residues: 23.4557 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5980 Z= 0.362 Angle : 0.736 10.417 8465 Z= 0.412 Chirality : 0.043 0.230 956 Planarity : 0.005 0.054 802 Dihedral : 29.904 179.147 1494 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 7.58 % Allowed : 26.01 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.35), residues: 516 helix: 1.56 (0.31), residues: 256 sheet: -0.61 (0.44), residues: 104 loop : 0.07 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP M 107 HIS 0.011 0.002 HIS N 86 PHE 0.017 0.003 PHE G 127 TYR 0.015 0.002 TYR N 76 ARG 0.006 0.001 ARG N 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 68 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7310 (tm-30) cc_final: 0.7006 (tp-100) REVERT: G 87 HIS cc_start: 0.5612 (OUTLIER) cc_final: 0.4730 (m90) REVERT: M 51 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7230 (p) REVERT: N 14 ARG cc_start: 0.5942 (ttp80) cc_final: 0.5557 (tmm160) outliers start: 30 outliers final: 27 residues processed: 89 average time/residue: 0.2138 time to fit residues: 23.8159 Evaluate side-chains 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.7011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5980 Z= 0.239 Angle : 0.659 10.875 8465 Z= 0.371 Chirality : 0.038 0.131 956 Planarity : 0.003 0.025 802 Dihedral : 29.673 178.425 1494 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 7.83 % Allowed : 26.26 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 516 helix: 1.84 (0.31), residues: 256 sheet: -0.72 (0.44), residues: 104 loop : 0.18 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP H 107 HIS 0.005 0.001 HIS N 86 PHE 0.017 0.002 PHE G 127 TYR 0.012 0.002 TYR N 76 ARG 0.006 0.001 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7244 (tm-30) cc_final: 0.7018 (tp-100) REVERT: G 87 HIS cc_start: 0.5476 (OUTLIER) cc_final: 0.4665 (m90) REVERT: M 51 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7034 (p) REVERT: N 14 ARG cc_start: 0.5962 (ttp80) cc_final: 0.5529 (tmm160) outliers start: 31 outliers final: 23 residues processed: 88 average time/residue: 0.2281 time to fit residues: 24.7874 Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5980 Z= 0.270 Angle : 0.680 11.165 8465 Z= 0.378 Chirality : 0.040 0.161 956 Planarity : 0.004 0.032 802 Dihedral : 29.858 179.919 1494 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 8.59 % Allowed : 26.77 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 516 helix: 1.70 (0.31), residues: 256 sheet: -0.81 (0.43), residues: 104 loop : 0.15 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 107 HIS 0.007 0.001 HIS N 86 PHE 0.018 0.002 PHE G 127 TYR 0.015 0.002 TYR N 76 ARG 0.004 0.001 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 64 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7278 (tm-30) cc_final: 0.7032 (tp-100) REVERT: G 87 HIS cc_start: 0.5519 (OUTLIER) cc_final: 0.4662 (m90) REVERT: H 48 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8743 (tt) REVERT: M 51 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7090 (p) REVERT: N 14 ARG cc_start: 0.5982 (ttp80) cc_final: 0.5642 (tmm160) outliers start: 34 outliers final: 28 residues processed: 90 average time/residue: 0.2435 time to fit residues: 26.6887 Evaluate side-chains 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 61 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.7514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5980 Z= 0.245 Angle : 0.657 11.274 8465 Z= 0.365 Chirality : 0.038 0.139 956 Planarity : 0.003 0.027 802 Dihedral : 29.828 179.525 1494 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 8.59 % Allowed : 26.26 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.36), residues: 516 helix: 1.79 (0.31), residues: 256 sheet: -0.79 (0.43), residues: 104 loop : 0.10 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP H 107 HIS 0.005 0.001 HIS N 84 PHE 0.018 0.002 PHE G 127 TYR 0.015 0.002 TYR N 76 ARG 0.004 0.000 ARG N 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 66 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7256 (tm-30) cc_final: 0.7030 (tp-100) REVERT: G 87 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4573 (m90) REVERT: M 51 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7050 (p) REVERT: M 104 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8216 (p) REVERT: N 14 ARG cc_start: 0.5918 (ttp80) cc_final: 0.5535 (tmm160) outliers start: 34 outliers final: 29 residues processed: 91 average time/residue: 0.2426 time to fit residues: 26.8740 Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 61 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5980 Z= 0.247 Angle : 0.656 10.402 8465 Z= 0.368 Chirality : 0.039 0.137 956 Planarity : 0.004 0.034 802 Dihedral : 29.869 179.972 1494 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 8.08 % Allowed : 27.02 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.35), residues: 516 helix: 1.66 (0.32), residues: 256 sheet: -0.84 (0.43), residues: 104 loop : 0.00 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 107 HIS 0.006 0.001 HIS N 86 PHE 0.018 0.002 PHE G 127 TYR 0.019 0.002 TYR H 76 ARG 0.004 0.001 ARG N 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 63 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7266 (tm-30) cc_final: 0.7032 (tp-100) REVERT: G 87 HIS cc_start: 0.5471 (OUTLIER) cc_final: 0.4590 (m90) REVERT: H 53 ARG cc_start: 0.8362 (ptp90) cc_final: 0.7958 (ptp90) REVERT: M 51 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7068 (p) REVERT: M 104 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8234 (p) REVERT: N 14 ARG cc_start: 0.5925 (ttp80) cc_final: 0.5614 (tmm160) outliers start: 32 outliers final: 26 residues processed: 85 average time/residue: 0.2388 time to fit residues: 24.8074 Evaluate side-chains 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 63 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.180044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.153671 restraints weight = 11174.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.156718 restraints weight = 19662.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.156625 restraints weight = 10769.951| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.7873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5980 Z= 0.218 Angle : 0.637 9.828 8465 Z= 0.355 Chirality : 0.037 0.122 956 Planarity : 0.003 0.041 802 Dihedral : 29.737 179.730 1494 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 7.07 % Allowed : 28.28 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.36), residues: 516 helix: 1.89 (0.32), residues: 256 sheet: -0.85 (0.42), residues: 104 loop : 0.01 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP H 107 HIS 0.005 0.001 HIS N 84 PHE 0.019 0.002 PHE G 127 TYR 0.015 0.002 TYR N 76 ARG 0.007 0.000 ARG H 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.63 seconds wall clock time: 27 minutes 1.66 seconds (1621.66 seconds total)