Starting phenix.real_space_refine on Thu Jul 2 01:59:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_32049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_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/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_32049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_32049.map" model { file = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_32049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2026/7vo9_32049_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.68, per 1000 atoms: 0.29 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 - 3.00 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: 0.49 Conformation dependent library (CDL) restraints added in 170.4 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: 0.68 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: 0.84 Time building geometry restraints manager: 0.65 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: 0.00 - 1.93: 6570 1.93 - 3.86: 1755 3.86 - 5.79: 125 5.79 - 7.72: 13 7.72 - 9.65: 2 Bond angle restraints: 8465 Sorted by residual: 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 angle pdb=" N GLU M 27 " pdb=" CA GLU M 27 " pdb=" C GLU M 27 " ideal model delta sigma weight residual 112.59 107.21 5.38 1.22e+00 6.72e-01 1.95e+01 angle pdb=" C ASP N 60 " pdb=" CA ASP N 60 " pdb=" CB ASP N 60 " ideal model delta sigma weight residual 110.79 117.76 -6.97 1.66e+00 3.63e-01 1.76e+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 - 0.097: 676 0.097 - 0.193: 247 0.193 - 0.290: 26 0.290 - 0.386: 4 0.386 - 0.483: 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 -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.83e+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 -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C3' DG A 20 " pdb=" C4' DG A 20 " pdb=" O3' DG A 20 " pdb=" C2' DG A 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.84e+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 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 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 : 0.020 0.570 6019 Z= 1.020 Angle : 1.721 27.760 8483 Z= 1.212 Chirality : 0.095 0.483 956 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG H 77 TYR 0.016 0.003 TYR G 117 PHE 0.014 0.003 PHE G 29 TRP 0.009 0.002 TRP N 107 HIS 0.040 0.003 HIS G 122 Details of bonding type rmsd/Z covalent geometry : bond 0.01111 / 0.85 ( 5980) covalent geometry : angle 1.56353 / 1.21 ( 8465) hydrogen bonds : bond 0.20605 / 22.90 ( 298) hydrogen bonds : angle 7.18813 / 9.25 ( 792) metal coordination : bond 0.21004 / 21.77 ( 39) metal coordination : angle 15.68208 / 23.99 ( 18) *********************** 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 to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.147 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: H 111 ILE cc_start: 0.7594 (pt) cc_final: 0.6962 (pt) REVERT: N 52 TYR cc_start: 0.7282 (m-80) cc_final: 0.6970 (m-80) REVERT: N 99 VAL cc_start: 0.8508 (m) cc_final: 0.8076 (t) outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.1200 time to fit residues: 22.8069 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.186791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.156894 restraints weight = 11480.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.161466 restraints weight = 17186.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.161048 restraints weight = 9262.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.161397 restraints weight = 7878.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.161790 restraints weight = 7090.541| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6019 Z= 0.239 Angle : 0.863 14.772 8483 Z= 0.482 Chirality : 0.050 0.312 956 Planarity : 0.005 0.062 802 Dihedral : 26.775 179.731 1494 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.79 % Allowed : 20.45 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.32), residues: 516 helix: 2.25 (0.28), residues: 256 sheet: 0.54 (0.49), residues: 96 loop : -0.18 (0.39), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 11 TYR 0.017 0.003 TYR M 117 PHE 0.014 0.003 PHE H 127 TRP 0.020 0.003 TRP N 107 HIS 0.009 0.002 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.24 ( 5980) covalent geometry : angle 0.79063 / 0.48 ( 8465) hydrogen bonds : bond 0.07654 / 8.68 ( 298) hydrogen bonds : angle 4.64688 / 5.76 ( 792) metal coordination : bond 0.01342 / 1.75 ( 39) metal coordination : angle 7.54735 / 9.90 ( 18) *********************** 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 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 126 ILE cc_start: 0.8145 (tp) cc_final: 0.7854 (pt) outliers start: 15 outliers final: 6 residues processed: 93 average time/residue: 0.0952 time to fit residues: 11.0066 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 107 TRP Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 4 optimal weight: 30.0000 chunk 52 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.184757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.156351 restraints weight = 11463.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.159920 restraints weight = 17876.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160569 restraints weight = 9789.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.160454 restraints weight = 8437.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.161105 restraints weight = 7091.081| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6019 Z= 0.185 Angle : 0.813 13.544 8483 Z= 0.453 Chirality : 0.049 0.330 956 Planarity : 0.004 0.040 802 Dihedral : 26.912 179.909 1494 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.79 % Allowed : 22.73 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.33), residues: 516 helix: 2.10 (0.29), residues: 256 sheet: 0.33 (0.48), residues: 96 loop : -0.32 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 11 TYR 0.025 0.002 TYR N 117 PHE 0.014 0.002 PHE N 29 TRP 0.026 0.004 TRP M 107 HIS 0.012 0.001 HIS N 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 ( 5980) covalent geometry : angle 0.74278 / 0.45 ( 8465) hydrogen bonds : bond 0.06001 / 6.74 ( 298) hydrogen bonds : angle 4.25290 / 5.34 ( 792) metal coordination : bond 0.00716 / 0.74 ( 39) metal coordination : angle 7.21842 / 10.45 ( 18) *********************** 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 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7038 (p) REVERT: M 126 ILE cc_start: 0.8403 (tp) cc_final: 0.8028 (pt) outliers start: 15 outliers final: 8 residues processed: 85 average time/residue: 0.0920 time to fit residues: 9.7334 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP 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 N residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.3980 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.185007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156939 restraints weight = 11269.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.159899 restraints weight = 19414.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.159439 restraints weight = 9030.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.159828 restraints weight = 7917.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.160049 restraints weight = 6982.027| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6019 Z= 0.190 Angle : 0.781 11.443 8483 Z= 0.444 Chirality : 0.049 0.329 956 Planarity : 0.004 0.045 802 Dihedral : 27.200 179.505 1494 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.05 % Allowed : 23.23 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.34), residues: 516 helix: 2.11 (0.30), residues: 256 sheet: -0.15 (0.46), residues: 104 loop : 0.19 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 11 TYR 0.009 0.002 TYR H 117 PHE 0.016 0.003 PHE G 127 TRP 0.024 0.003 TRP H 107 HIS 0.012 0.001 HIS N 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 ( 5980) covalent geometry : angle 0.73648 / 0.44 ( 8465) hydrogen bonds : bond 0.05590 / 6.29 ( 298) hydrogen bonds : angle 4.22791 / 5.34 ( 792) metal coordination : bond 0.00890 / 1.20 ( 39) metal coordination : angle 5.67961 / 8.19 ( 18) *********************** 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 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 104 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8415 (p) REVERT: M 126 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8142 (pt) outliers start: 20 outliers final: 15 residues processed: 80 average time/residue: 0.0809 time to fit residues: 8.2559 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 99 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 126 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.183078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.154587 restraints weight = 11295.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.158586 restraints weight = 18964.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158589 restraints weight = 9207.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158869 restraints weight = 7603.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.159313 restraints weight = 7176.412| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6019 Z= 0.169 Angle : 0.753 10.586 8483 Z= 0.429 Chirality : 0.048 0.332 956 Planarity : 0.004 0.026 802 Dihedral : 27.495 179.200 1494 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.05 % Allowed : 24.24 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.35), residues: 516 helix: 2.18 (0.31), residues: 256 sheet: -0.23 (0.46), residues: 104 loop : 0.34 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.008 0.001 TYR N 76 PHE 0.029 0.003 PHE N 29 TRP 0.025 0.002 TRP H 107 HIS 0.005 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 ( 5980) covalent geometry : angle 0.71438 / 0.43 ( 8465) hydrogen bonds : bond 0.05348 / 5.98 ( 298) hydrogen bonds : angle 4.05229 / 5.12 ( 792) metal coordination : bond 0.00482 / 0.58 ( 39) metal coordination : angle 5.23784 / 7.35 ( 18) *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7212 (p) REVERT: M 104 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8366 (p) REVERT: M 126 ILE cc_start: 0.8388 (tp) cc_final: 0.8123 (pt) outliers start: 20 outliers final: 13 residues processed: 81 average time/residue: 0.0742 time to fit residues: 7.6639 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 99 VAL 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 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 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.180970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.153908 restraints weight = 11197.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.155997 restraints weight = 21042.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.156988 restraints weight = 10510.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.157067 restraints weight = 8060.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157514 restraints weight = 7914.491| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6019 Z= 0.220 Angle : 0.787 9.588 8483 Z= 0.445 Chirality : 0.050 0.330 956 Planarity : 0.004 0.043 802 Dihedral : 27.841 178.896 1494 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.31 % Allowed : 24.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.35), residues: 516 helix: 2.03 (0.32), residues: 256 sheet: -0.46 (0.46), residues: 104 loop : 0.32 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 53 TYR 0.014 0.002 TYR N 117 PHE 0.018 0.003 PHE G 127 TRP 0.033 0.003 TRP H 107 HIS 0.011 0.002 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 ( 5980) covalent geometry : angle 0.75593 / 0.44 ( 8465) hydrogen bonds : bond 0.05840 / 6.42 ( 298) hydrogen bonds : angle 4.17772 / 5.25 ( 792) metal coordination : bond 0.00566 / 0.61 ( 39) metal coordination : angle 4.82900 / 6.69 ( 18) *********************** 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7280 (p) REVERT: M 104 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8460 (p) REVERT: M 126 ILE cc_start: 0.8395 (tp) cc_final: 0.8149 (pt) outliers start: 25 outliers final: 19 residues processed: 78 average time/residue: 0.0767 time to fit residues: 7.3997 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL 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 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 99 VAL 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 48 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 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.180269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.156565 restraints weight = 11104.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.155580 restraints weight = 20202.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.153924 restraints weight = 11191.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.154506 restraints weight = 9943.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154760 restraints weight = 7790.419| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6019 Z= 0.211 Angle : 0.810 11.754 8483 Z= 0.443 Chirality : 0.050 0.330 956 Planarity : 0.005 0.039 802 Dihedral : 28.231 177.629 1494 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.57 % Allowed : 24.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.36), residues: 516 helix: 1.94 (0.31), residues: 256 sheet: -0.64 (0.46), residues: 104 loop : 0.31 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 11 TYR 0.016 0.002 TYR N 52 PHE 0.019 0.002 PHE G 127 TRP 0.042 0.003 TRP H 107 HIS 0.009 0.002 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 ( 5980) covalent geometry : angle 0.76316 / 0.44 ( 8465) hydrogen bonds : bond 0.05955 / 6.44 ( 298) hydrogen bonds : angle 4.09844 / 5.18 ( 792) metal coordination : bond 0.00802 / 0.88 ( 39) metal coordination : angle 5.93818 / 8.87 ( 18) *********************** 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 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.7830 (p) REVERT: M 104 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8429 (p) REVERT: M 126 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8005 (pt) outliers start: 26 outliers final: 19 residues processed: 80 average time/residue: 0.0825 time to fit residues: 8.1699 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL 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 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 126 ILE 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 126 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.180984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.154665 restraints weight = 11054.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.156694 restraints weight = 18462.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.156362 restraints weight = 10035.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.156521 restraints weight = 8510.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.156671 restraints weight = 7897.615| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6019 Z= 0.178 Angle : 0.788 11.197 8483 Z= 0.438 Chirality : 0.049 0.329 956 Planarity : 0.004 0.022 802 Dihedral : 28.395 176.543 1494 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.31 % Allowed : 24.75 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.36), residues: 516 helix: 1.99 (0.32), residues: 256 sheet: -0.62 (0.46), residues: 104 loop : 0.27 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 53 TYR 0.008 0.002 TYR H 117 PHE 0.018 0.002 PHE G 127 TRP 0.043 0.003 TRP H 107 HIS 0.006 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 ( 5980) covalent geometry : angle 0.74924 / 0.44 ( 8465) hydrogen bonds : bond 0.05477 / 5.94 ( 298) hydrogen bonds : angle 4.05025 / 5.06 ( 792) metal coordination : bond 0.00538 / 0.57 ( 39) metal coordination : angle 5.32443 / 7.94 ( 18) *********************** 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 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7404 (p) REVERT: M 65 ASP cc_start: 0.7158 (m-30) cc_final: 0.6687 (m-30) REVERT: M 104 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8385 (p) REVERT: M 126 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7979 (pt) outliers start: 25 outliers final: 21 residues processed: 82 average time/residue: 0.0953 time to fit residues: 9.6680 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL 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 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL 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 126 ILE 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 74 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.177354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.150480 restraints weight = 11118.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152319 restraints weight = 21417.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.152809 restraints weight = 10980.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.153183 restraints weight = 8453.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153627 restraints weight = 7790.458| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6019 Z= 0.205 Angle : 0.816 10.288 8483 Z= 0.451 Chirality : 0.050 0.327 956 Planarity : 0.005 0.063 802 Dihedral : 28.660 175.518 1494 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.82 % Allowed : 25.25 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.35), residues: 516 helix: 1.84 (0.31), residues: 256 sheet: -0.69 (0.46), residues: 104 loop : 0.23 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 30 TYR 0.009 0.002 TYR N 76 PHE 0.022 0.003 PHE G 29 TRP 0.048 0.003 TRP H 107 HIS 0.009 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 ( 5980) covalent geometry : angle 0.78141 / 0.45 ( 8465) hydrogen bonds : bond 0.05735 / 6.24 ( 298) hydrogen bonds : angle 4.09574 / 5.14 ( 792) metal coordination : bond 0.00541 / 0.59 ( 39) metal coordination : angle 5.13331 / 7.49 ( 18) *********************** 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 LYS cc_start: 0.7642 (mttp) cc_final: 0.7302 (mtmm) REVERT: M 51 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7261 (p) REVERT: M 65 ASP cc_start: 0.7359 (m-30) cc_final: 0.6871 (m-30) REVERT: M 104 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (p) REVERT: M 126 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7988 (pt) outliers start: 27 outliers final: 22 residues processed: 84 average time/residue: 0.1042 time to fit residues: 10.7267 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 24 GLN 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 88 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL 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 126 ILE 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 74 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.151197 restraints weight = 11313.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.153721 restraints weight = 20509.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.154700 restraints weight = 11692.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155208 restraints weight = 8481.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155830 restraints weight = 7724.935| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6019 Z= 0.177 Angle : 0.820 10.719 8483 Z= 0.448 Chirality : 0.050 0.327 956 Planarity : 0.005 0.079 802 Dihedral : 28.793 177.059 1494 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.31 % Allowed : 26.01 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.35), residues: 516 helix: 1.85 (0.31), residues: 256 sheet: -0.64 (0.46), residues: 104 loop : 0.08 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG N 91 TYR 0.008 0.002 TYR H 76 PHE 0.018 0.003 PHE G 127 TRP 0.045 0.003 TRP H 107 HIS 0.006 0.001 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 ( 5980) covalent geometry : angle 0.78812 / 0.45 ( 8465) hydrogen bonds : bond 0.05291 / 5.74 ( 298) hydrogen bonds : angle 3.98192 / 4.92 ( 792) metal coordination : bond 0.00461 / 0.50 ( 39) metal coordination : angle 4.97754 / 7.25 ( 18) ********************** 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 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7376 (tm-30) cc_final: 0.6998 (tp-100) REVERT: M 51 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7026 (p) REVERT: M 65 ASP cc_start: 0.7180 (m-30) cc_final: 0.6736 (m-30) REVERT: M 104 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8342 (p) REVERT: M 126 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7946 (pt) outliers start: 25 outliers final: 21 residues processed: 83 average time/residue: 0.0786 time to fit residues: 8.0372 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL 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 126 ILE 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 74 SER Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.152443 restraints weight = 11132.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.155155 restraints weight = 19796.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.156049 restraints weight = 11333.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.156230 restraints weight = 8507.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.156581 restraints weight = 8489.145| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6019 Z= 0.182 Angle : 0.826 11.847 8483 Z= 0.451 Chirality : 0.050 0.324 956 Planarity : 0.005 0.057 802 Dihedral : 28.973 178.219 1494 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.82 % Allowed : 26.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.35), residues: 516 helix: 1.95 (0.32), residues: 256 sheet: -0.63 (0.45), residues: 104 loop : 0.02 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 91 TYR 0.009 0.002 TYR H 76 PHE 0.018 0.003 PHE G 127 TRP 0.068 0.004 TRP H 107 HIS 0.006 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 ( 5980) covalent geometry : angle 0.79633 / 0.45 ( 8465) hydrogen bonds : bond 0.05337 / 5.77 ( 298) hydrogen bonds : angle 4.08115 / 5.04 ( 792) metal coordination : bond 0.00444 / 0.48 ( 39) metal coordination : angle 4.80111 / 6.89 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 910.70 seconds wall clock time: 16 minutes 25.07 seconds (985.07 seconds total)