Starting phenix.real_space_refine on Thu Sep 10 23:46:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/09_2026/7vo9_32049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vo9_32049/09_2026/7vo9_32049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/09_2026/7vo9_32049_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vo9_32049/09_2026/7vo9_32049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/09_2026/7vo9_32049.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 1.52, per 1000 atoms: 0.27 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: 0.55 Conformation dependent library (CDL) restraints added in 161.0 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: 0.78 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: 0.92 Time building geometry restraints manager: 0.66 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=" O3' DG A 32 " pdb=" P DT A 33 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.37e+01 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 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 6564 1.93 - 3.86: 1758 3.86 - 5.79: 128 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=" C3' DG A 32 " pdb=" O3' DG A 32 " pdb=" P DT A 33 " ideal model delta sigma weight residual 119.70 124.92 -5.22 1.20e+00 6.94e-01 1.89e+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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.100 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- 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= 1.023 Angle : 1.724 27.760 8483 Z= 1.217 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 / 0.86 ( 5980) covalent geometry : angle 1.56731 / 1.21 ( 8465) hydrogen bonds : bond 0.20605 / 23.01 ( 298) hydrogen bonds : angle 7.18813 / 9.24 ( 792) metal coordination : bond 0.21004 / 21.89 ( 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 : 0.172 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 56 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6324 (mt0) 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: 0.1290 time to fit residues: 24.5805 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.185326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.155615 restraints weight = 11490.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.158832 restraints weight = 18191.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.160047 restraints weight = 10811.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.159774 restraints weight = 8619.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.160405 restraints weight = 7362.757| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6019 Z= 0.227 Angle : 0.868 14.659 8483 Z= 0.484 Chirality : 0.051 0.334 956 Planarity : 0.006 0.064 802 Dihedral : 26.775 179.813 1494 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.54 % Allowed : 20.45 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.24 (0.28), residues: 256 sheet: 0.56 (0.49), residues: 96 loop : -0.17 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 11 TYR 0.017 0.003 TYR M 117 PHE 0.016 0.003 PHE H 127 TRP 0.022 0.003 TRP N 107 HIS 0.008 0.002 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 ( 5980) covalent geometry : angle 0.79752 / 0.48 ( 8465) hydrogen bonds : bond 0.07614 / 8.64 ( 298) hydrogen bonds : angle 4.61841 / 5.72 ( 792) metal coordination : bond 0.01373 / 1.70 ( 39) metal coordination : angle 7.46862 / 9.80 ( 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 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 126 ILE cc_start: 0.8144 (tp) cc_final: 0.7850 (pt) outliers start: 14 outliers final: 6 residues processed: 92 average time/residue: 0.0985 time to fit residues: 11.2057 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 52 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 115 HIS ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.186104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.159256 restraints weight = 11370.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.163055 restraints weight = 17455.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.162334 restraints weight = 9235.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.162642 restraints weight = 7703.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.162848 restraints weight = 6391.900| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3782 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= 0.194 Angle : 0.831 14.576 8483 Z= 0.458 Chirality : 0.050 0.359 956 Planarity : 0.005 0.070 802 Dihedral : 26.950 179.636 1494 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.29 % Allowed : 22.22 % 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: 1.47 (0.33), residues: 516 helix: 2.05 (0.29), residues: 256 sheet: 0.28 (0.48), residues: 96 loop : -0.25 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 14 TYR 0.029 0.002 TYR N 117 PHE 0.014 0.002 PHE G 127 TRP 0.024 0.004 TRP M 107 HIS 0.011 0.001 HIS N 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 ( 5980) covalent geometry : angle 0.75324 / 0.45 ( 8465) hydrogen bonds : bond 0.05961 / 6.69 ( 298) hydrogen bonds : angle 4.22090 / 5.32 ( 792) metal coordination : bond 0.00696 / 0.74 ( 39) metal coordination : angle 7.65443 / 11.27 ( 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 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.172 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: H 56 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6824 (mm-40) REVERT: M 51 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7681 (p) REVERT: M 104 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8394 (p) REVERT: M 126 ILE cc_start: 0.8409 (tp) cc_final: 0.8033 (pt) outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.1101 time to fit residues: 11.8866 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 H residue 50 THR 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 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4570 r_free = 0.4570 target = 0.184702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.156408 restraints weight = 11247.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.159359 restraints weight = 19591.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158617 restraints weight = 8933.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.159094 restraints weight = 8347.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.159248 restraints weight = 6915.482| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6019 Z= 0.188 Angle : 0.784 11.290 8483 Z= 0.442 Chirality : 0.050 0.355 956 Planarity : 0.004 0.025 802 Dihedral : 27.310 178.782 1494 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 5.56 % Allowed : 22.73 % 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: 1.64 (0.35), residues: 516 helix: 2.20 (0.31), residues: 256 sheet: -0.15 (0.47), residues: 104 loop : 0.24 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 14 TYR 0.010 0.001 TYR N 117 PHE 0.017 0.002 PHE G 127 TRP 0.023 0.002 TRP H 107 HIS 0.007 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 ( 5980) covalent geometry : angle 0.74237 / 0.44 ( 8465) hydrogen bonds : bond 0.05500 / 6.18 ( 298) hydrogen bonds : angle 4.07232 / 5.14 ( 792) metal coordination : bond 0.01266 / 1.67 ( 39) metal coordination : angle 5.49763 / 7.83 ( 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 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: M 126 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (pt) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.1045 time to fit residues: 10.9857 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 88 LEU 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 126 ILE 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 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: 0.4980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.183669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154458 restraints weight = 11394.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158456 restraints weight = 20025.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.158667 restraints weight = 9988.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.158827 restraints weight = 8197.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.159630 restraints weight = 7507.914| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6019 Z= 0.158 Angle : 0.744 10.586 8483 Z= 0.421 Chirality : 0.049 0.361 956 Planarity : 0.003 0.022 802 Dihedral : 27.442 178.615 1494 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.04 % Allowed : 25.76 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.35), residues: 516 helix: 2.33 (0.31), residues: 256 sheet: -0.22 (0.47), residues: 104 loop : 0.36 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 11 TYR 0.013 0.001 TYR N 117 PHE 0.029 0.003 PHE N 29 TRP 0.020 0.002 TRP H 107 HIS 0.005 0.001 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 ( 5980) covalent geometry : angle 0.70161 / 0.42 ( 8465) hydrogen bonds : bond 0.05177 / 5.77 ( 298) hydrogen bonds : angle 3.87234 / 4.89 ( 792) metal coordination : bond 0.00503 / 0.61 ( 39) metal coordination : angle 5.40774 / 7.65 ( 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: 16 poor density : 70 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (p) REVERT: M 126 ILE cc_start: 0.8324 (tp) cc_final: 0.8085 (pt) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1121 time to fit residues: 11.1983 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 89 VAL 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 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: 4.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.177117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.150141 restraints weight = 11097.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.152220 restraints weight = 19927.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.151840 restraints weight = 10953.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.152259 restraints weight = 9047.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.152791 restraints weight = 7506.605| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6019 Z= 0.272 Angle : 0.869 12.356 8483 Z= 0.474 Chirality : 0.054 0.354 956 Planarity : 0.006 0.073 802 Dihedral : 28.042 179.661 1494 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.82 % Allowed : 23.74 % 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 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: 1.11 (0.35), residues: 516 helix: 1.76 (0.31), residues: 256 sheet: -0.58 (0.46), residues: 104 loop : 0.12 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 68 TYR 0.012 0.002 TYR N 117 PHE 0.017 0.003 PHE G 127 TRP 0.028 0.002 TRP H 107 HIS 0.018 0.002 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.27 ( 5980) covalent geometry : angle 0.82602 / 0.47 ( 8465) hydrogen bonds : bond 0.06625 / 7.25 ( 298) hydrogen bonds : angle 4.36040 / 5.54 ( 792) metal coordination : bond 0.00810 / 0.85 ( 39) metal coordination : angle 5.94407 / 8.79 ( 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: 27 poor density : 58 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.7791 (p) REVERT: M 126 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (pt) outliers start: 27 outliers final: 21 residues processed: 77 average time/residue: 0.1088 time to fit residues: 10.4593 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 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 126 ILE 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 89 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: 2.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.179765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.150600 restraints weight = 11162.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.154179 restraints weight = 19509.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.154645 restraints weight = 11011.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.154912 restraints weight = 8508.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.155588 restraints weight = 7389.906| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6019 Z= 0.171 Angle : 0.761 10.033 8483 Z= 0.421 Chirality : 0.050 0.358 956 Planarity : 0.004 0.053 802 Dihedral : 28.206 179.833 1494 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 6.06 % Allowed : 23.99 % Favored : 69.95 % 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: 1.37 (0.36), residues: 516 helix: 2.08 (0.32), residues: 256 sheet: -0.60 (0.46), residues: 104 loop : 0.15 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 11 TYR 0.009 0.002 TYR N 76 PHE 0.018 0.002 PHE G 127 TRP 0.027 0.002 TRP H 107 HIS 0.006 0.001 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 ( 5980) covalent geometry : angle 0.71796 / 0.42 ( 8465) hydrogen bonds : bond 0.05487 / 5.98 ( 298) hydrogen bonds : angle 3.92878 / 4.99 ( 792) metal coordination : bond 0.00577 / 0.63 ( 39) metal coordination : angle 5.51955 / 8.20 ( 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 11 ARG cc_start: 0.5828 (ttp-170) cc_final: 0.5460 (tmm-80) REVERT: M 51 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7207 (p) REVERT: M 126 ILE cc_start: 0.8371 (tp) cc_final: 0.8103 (pt) outliers start: 24 outliers final: 21 residues processed: 77 average time/residue: 0.0911 time to fit residues: 8.7579 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 30 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 126 ILE 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 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 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.179480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.155748 restraints weight = 10964.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.156050 restraints weight = 19532.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155484 restraints weight = 9937.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156238 restraints weight = 7844.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156495 restraints weight = 6520.121| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6019 Z= 0.176 Angle : 0.770 10.210 8483 Z= 0.425 Chirality : 0.050 0.355 956 Planarity : 0.004 0.067 802 Dihedral : 28.416 177.600 1494 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 6.57 % Allowed : 24.75 % Favored : 68.69 % 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: 1.38 (0.36), residues: 516 helix: 2.09 (0.32), residues: 256 sheet: -0.59 (0.46), residues: 104 loop : 0.16 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 30 TYR 0.009 0.002 TYR N 117 PHE 0.018 0.002 PHE G 127 TRP 0.028 0.002 TRP H 107 HIS 0.006 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 ( 5980) covalent geometry : angle 0.73303 / 0.42 ( 8465) hydrogen bonds : bond 0.05454 / 5.87 ( 298) hydrogen bonds : angle 3.91289 / 4.90 ( 792) metal coordination : bond 0.00475 / 0.51 ( 39) metal coordination : angle 5.16384 / 7.53 ( 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: 26 poor density : 62 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 11 ARG cc_start: 0.5828 (ttp-170) cc_final: 0.5475 (tmm-80) REVERT: M 51 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7279 (p) REVERT: M 65 ASP cc_start: 0.7094 (m-30) cc_final: 0.6661 (m-30) REVERT: M 126 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8176 (pt) REVERT: N 91 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.5405 (mtm-85) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.1050 time to fit residues: 10.3083 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 : 0.173 ------------------------------------------------------------------------------- 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 30 ARG 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 89 VAL Chi-restraints excluded: chain M residue 99 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.177492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148874 restraints weight = 11050.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.150807 restraints weight = 20723.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152039 restraints weight = 11644.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152079 restraints weight = 8958.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.152727 restraints weight = 8833.883| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6019 Z= 0.281 Angle : 0.885 9.911 8483 Z= 0.477 Chirality : 0.054 0.347 956 Planarity : 0.006 0.083 802 Dihedral : 28.910 174.770 1494 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 6.57 % Allowed : 25.51 % 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: 0.72 (0.35), residues: 516 helix: 1.63 (0.31), residues: 256 sheet: -0.98 (0.44), residues: 104 loop : -0.23 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 11 TYR 0.013 0.003 TYR N 76 PHE 0.020 0.004 PHE N 29 TRP 0.034 0.003 TRP H 107 HIS 0.015 0.002 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 ( 5980) covalent geometry : angle 0.85339 / 0.48 ( 8465) hydrogen bonds : bond 0.06560 / 7.08 ( 298) hydrogen bonds : angle 4.28530 / 5.41 ( 792) metal coordination : bond 0.00705 / 0.74 ( 39) metal coordination : angle 5.13428 / 7.28 ( 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6986 (tp-100) REVERT: M 51 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7731 (t) REVERT: M 104 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8343 (p) REVERT: M 126 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8080 (pt) REVERT: N 11 ARG cc_start: 0.6398 (mmp80) cc_final: 0.5526 (ttt-90) REVERT: N 91 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5535 (mtm-85) outliers start: 26 outliers final: 21 residues processed: 77 average time/residue: 0.1068 time to fit residues: 10.1493 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 M residue 19 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 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 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 5 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.178073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154817 restraints weight = 11281.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.150948 restraints weight = 21068.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.152152 restraints weight = 12896.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.153116 restraints weight = 9906.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.153392 restraints weight = 7303.366| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6019 Z= 0.180 Angle : 0.821 12.359 8483 Z= 0.446 Chirality : 0.051 0.348 956 Planarity : 0.006 0.132 802 Dihedral : 28.952 175.910 1494 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.06 % Allowed : 26.52 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.35), residues: 516 helix: 1.65 (0.32), residues: 256 sheet: -0.88 (0.44), residues: 104 loop : -0.06 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 30 TYR 0.009 0.002 TYR N 117 PHE 0.019 0.003 PHE G 127 TRP 0.031 0.002 TRP H 107 HIS 0.006 0.001 HIS N 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 ( 5980) covalent geometry : angle 0.78845 / 0.44 ( 8465) hydrogen bonds : bond 0.05337 / 5.71 ( 298) hydrogen bonds : angle 4.02737 / 5.07 ( 792) metal coordination : bond 0.00464 / 0.51 ( 39) metal coordination : angle 5.01783 / 7.20 ( 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7106 (tp-100) REVERT: M 51 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7175 (p) REVERT: M 65 ASP cc_start: 0.7059 (m-30) cc_final: 0.6617 (m-30) REVERT: M 126 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (pt) REVERT: N 91 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5529 (mtm-85) outliers start: 24 outliers final: 20 residues processed: 78 average time/residue: 0.1093 time to fit residues: 10.5608 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 30 ARG Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 19 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 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 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: 0.8980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.177966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.153150 restraints weight = 10964.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155381 restraints weight = 19676.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.154712 restraints weight = 9235.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155309 restraints weight = 7679.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155495 restraints weight = 6839.531| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6019 Z= 0.177 Angle : 0.811 10.555 8483 Z= 0.440 Chirality : 0.052 0.344 956 Planarity : 0.004 0.029 802 Dihedral : 29.071 176.640 1494 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.31 % Allowed : 26.52 % Favored : 67.17 % 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: 0.87 (0.35), residues: 516 helix: 1.73 (0.32), residues: 256 sheet: -0.86 (0.44), residues: 104 loop : -0.15 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 30 TYR 0.009 0.002 TYR N 117 PHE 0.019 0.002 PHE G 127 TRP 0.031 0.002 TRP H 107 HIS 0.006 0.001 HIS N 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 ( 5980) covalent geometry : angle 0.78020 / 0.44 ( 8465) hydrogen bonds : bond 0.05299 / 5.65 ( 298) hydrogen bonds : angle 4.01582 / 5.07 ( 792) metal coordination : bond 0.00460 / 0.50 ( 39) metal coordination : angle 4.84305 / 6.88 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1075.31 seconds wall clock time: 19 minutes 25.15 seconds (1165.15 seconds total)