Starting phenix.real_space_refine on Tue Mar 3 13:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/03_2026/7vo9_32049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/03_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_32049/03_2026/7vo9_32049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_2026/7vo9_32049_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_2026/7vo9_32049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_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-dev-5986/lib/python3.9/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: 1.24, per 1000 atoms: 0.22 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: 0.36 Conformation dependent library (CDL) restraints added in 223.7 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: 0.77 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: 0.85 Time building geometry restraints manager: 0.49 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 - 1.61: 6021 1.61 - 3.22: 2000 3.22 - 4.83: 410 4.83 - 6.44: 28 6.44 - 8.05: 6 Bond angle restraints: 8465 Sorted by residual: angle pdb=" C4' DT A 33 " pdb=" C3' DT A 33 " pdb=" O3' DT A 33 " ideal model delta sigma weight residual 110.00 118.05 -8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" O3' DT B 82 " pdb=" C3' DT B 82 " pdb=" C2' DT B 82 " ideal model delta sigma weight residual 111.50 119.05 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CA HIS M 86 " pdb=" CB HIS M 86 " pdb=" CG HIS M 86 " ideal model delta sigma weight residual 113.80 109.06 4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" N GLY G 94 " pdb=" CA GLY G 94 " pdb=" C GLY G 94 " ideal model delta sigma weight residual 115.30 108.81 6.49 1.39e+00 5.18e-01 2.18e+01 angle pdb=" N GLY M 94 " pdb=" CA GLY M 94 " pdb=" C GLY M 94 " ideal model delta sigma weight residual 115.36 109.19 6.17 1.33e+00 5.65e-01 2.15e+01 ... (remaining 8460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 3015 35.05 - 70.09: 280 70.09 - 105.13: 2 105.13 - 140.18: 7 140.18 - 175.22: 6 Dihedral angle restraints: 3310 sinusoidal: 1818 harmonic: 1492 Sorted by residual: dihedral pdb=" C ASP N 60 " pdb=" N ASP N 60 " pdb=" CA ASP N 60 " pdb=" CB ASP N 60 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C4' DG A 11 " pdb=" C3' DG A 11 " pdb=" O3' DG A 11 " pdb=" P DA A 12 " ideal model delta sinusoidal sigma weight residual -140.00 35.22 -175.22 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC A 1 " pdb=" C3' DC A 1 " pdb=" O3' DC A 1 " pdb=" P DA A 2 " ideal model delta sinusoidal sigma weight residual 220.00 46.22 173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 3307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 645 0.083 - 0.165: 255 0.165 - 0.248: 50 0.248 - 0.330: 3 0.330 - 0.412: 3 Chirality restraints: 956 Sorted by residual: chirality pdb=" C3' DT B 82 " pdb=" C4' DT B 82 " pdb=" O3' DT B 82 " pdb=" C2' DT B 82 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C3' DG B 56 " pdb=" C4' DG B 56 " pdb=" O3' DG B 56 " pdb=" C2' DG B 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ASP N 60 " pdb=" N ASP N 60 " pdb=" C ASP N 60 " pdb=" CB ASP N 60 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 953 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 122 " 0.011 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG HIS G 122 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS G 122 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS G 122 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS G 122 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS G 122 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS M 86 " -0.019 2.00e-02 2.50e+03 1.93e-02 5.56e+00 pdb=" CG HIS M 86 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS M 86 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 72 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C GLY M 72 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY M 72 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU M 73 " 0.012 2.00e-02 2.50e+03 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 179 2.68 - 3.23: 4633 3.23 - 3.79: 10248 3.79 - 4.34: 13092 4.34 - 4.90: 18444 Nonbonded interactions: 46596 Sorted by model distance: nonbonded pdb=" OD2 ASP H 65 " pdb="ZN ZN H 202 " model vdw 2.124 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.230 2.230 nonbonded pdb=" C2' DG B 42 " pdb=" O5' DT B 43 " model vdw 2.332 3.440 nonbonded pdb=" C2' DT B 71 " pdb=" N7 DG B 72 " model vdw 2.439 3.520 nonbonded pdb=" O ILE M 111 " pdb=" ND1 HIS M 115 " model vdw 2.496 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: 2.190 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.490 Find NCS groups from input model: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.570 6019 Z= 1.013 Angle : 1.736 27.760 8483 Z= 1.211 Chirality : 0.088 0.412 956 Planarity : 0.004 0.027 802 Dihedral : 23.203 175.224 2350 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.76 % Allowed : 10.61 % Favored : 88.64 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.01124 ( 5980) covalent geometry : angle 1.58019 ( 8465) hydrogen bonds : bond 0.20605 ( 298) hydrogen bonds : angle 7.18813 ( 792) metal coordination : bond 0.21004 ( 39) metal coordination : angle 15.68208 ( 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 : 0.164 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: 0.1339 time to fit residues: 25.2668 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 : 0.144 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 HIS M 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.184048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.157145 restraints weight = 11407.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.160278 restraints weight = 20641.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.160599 restraints weight = 10428.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.160996 restraints weight = 8017.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.161476 restraints weight = 7453.884| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6019 Z= 0.223 Angle : 0.772 9.097 8483 Z= 0.427 Chirality : 0.044 0.155 956 Planarity : 0.005 0.045 802 Dihedral : 27.737 179.758 1494 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.04 % Allowed : 21.46 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.20 (0.34), residues: 516 helix: 2.66 (0.29), residues: 256 sheet: 0.21 (0.46), residues: 104 loop : 0.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 77 TYR 0.014 0.002 TYR N 117 PHE 0.016 0.003 PHE G 127 TRP 0.016 0.003 TRP N 107 HIS 0.009 0.002 HIS H 86 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 5980) covalent geometry : angle 0.72878 ( 8465) hydrogen bonds : bond 0.05692 ( 298) hydrogen bonds : angle 4.14545 ( 792) metal coordination : bond 0.00690 ( 39) metal coordination : angle 5.57895 ( 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: 16 poor density : 83 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 126 ILE cc_start: 0.8155 (tp) cc_final: 0.7933 (pt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.1058 time to fit residues: 12.1059 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 H residue 99 VAL Chi-restraints excluded: chain M residue 84 HIS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.177956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.151095 restraints weight = 11223.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.152293 restraints weight = 18780.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.153688 restraints weight = 11457.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.153426 restraints weight = 8508.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.153839 restraints weight = 8494.342| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6019 Z= 0.246 Angle : 0.778 12.973 8483 Z= 0.417 Chirality : 0.043 0.147 956 Planarity : 0.005 0.045 802 Dihedral : 28.957 178.069 1494 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.57 % Allowed : 20.71 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.35), residues: 516 helix: 2.03 (0.30), residues: 256 sheet: -0.15 (0.47), residues: 104 loop : 0.25 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 68 TYR 0.011 0.002 TYR H 117 PHE 0.017 0.002 PHE G 127 TRP 0.030 0.004 TRP M 107 HIS 0.011 0.002 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 5980) covalent geometry : angle 0.73031 ( 8465) hydrogen bonds : bond 0.06129 ( 298) hydrogen bonds : angle 4.18998 ( 792) metal coordination : bond 0.00623 ( 39) metal coordination : angle 5.84455 ( 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 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5262 (m90) REVERT: M 65 ASP cc_start: 0.7273 (m-30) cc_final: 0.6893 (m-30) REVERT: N 14 ARG cc_start: 0.5663 (ttp80) cc_final: 0.5420 (tmm160) outliers start: 26 outliers final: 18 residues processed: 92 average time/residue: 0.1142 time to fit residues: 12.7442 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 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 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 56 GLN 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 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 69 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.180724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.154232 restraints weight = 11262.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.156723 restraints weight = 20873.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.156961 restraints weight = 10218.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.157260 restraints weight = 7955.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.157427 restraints weight = 7568.637| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6019 Z= 0.173 Angle : 0.699 11.105 8483 Z= 0.383 Chirality : 0.040 0.173 956 Planarity : 0.004 0.022 802 Dihedral : 29.059 177.890 1494 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.05 % Allowed : 23.48 % Favored : 71.46 % 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: 1.66 (0.35), residues: 516 helix: 2.20 (0.31), residues: 256 sheet: -0.20 (0.47), residues: 104 loop : 0.31 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.011 0.002 TYR N 117 PHE 0.015 0.002 PHE G 127 TRP 0.036 0.004 TRP M 107 HIS 0.005 0.001 HIS N 84 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5980) covalent geometry : angle 0.67063 ( 8465) hydrogen bonds : bond 0.05034 ( 298) hydrogen bonds : angle 3.82019 ( 792) metal coordination : bond 0.00405 ( 39) metal coordination : angle 4.32380 ( 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 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6886 (tp-100) REVERT: G 87 HIS cc_start: 0.5841 (OUTLIER) cc_final: 0.5425 (m90) REVERT: H 56 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: M 65 ASP cc_start: 0.7135 (m-30) cc_final: 0.6845 (m-30) REVERT: M 104 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8274 (p) REVERT: N 14 ARG cc_start: 0.5795 (ttp80) cc_final: 0.5482 (tmm160) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.1072 time to fit residues: 12.2753 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 66 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 69 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.181044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.152284 restraints weight = 11454.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.154480 restraints weight = 19198.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155824 restraints weight = 11021.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.155596 restraints weight = 8850.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.156243 restraints weight = 8109.797| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6019 Z= 0.180 Angle : 0.691 10.853 8483 Z= 0.380 Chirality : 0.039 0.138 956 Planarity : 0.004 0.028 802 Dihedral : 29.328 179.016 1494 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.81 % Allowed : 26.77 % 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: 1.37 (0.35), residues: 516 helix: 1.97 (0.30), residues: 256 sheet: -0.50 (0.46), residues: 104 loop : 0.30 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 11 TYR 0.011 0.002 TYR N 117 PHE 0.016 0.002 PHE G 127 TRP 0.055 0.005 TRP M 107 HIS 0.005 0.001 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5980) covalent geometry : angle 0.67021 ( 8465) hydrogen bonds : bond 0.04753 ( 298) hydrogen bonds : angle 3.89914 ( 792) metal coordination : bond 0.00421 ( 39) metal coordination : angle 3.67522 ( 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 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6991 (tp-100) REVERT: G 87 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5196 (m90) REVERT: M 51 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7350 (p) REVERT: M 65 ASP cc_start: 0.7106 (m-30) cc_final: 0.6853 (m-30) REVERT: M 104 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8137 (p) REVERT: N 14 ARG cc_start: 0.5931 (ttp80) cc_final: 0.5673 (tmm160) outliers start: 23 outliers final: 12 residues processed: 91 average time/residue: 0.0988 time to fit residues: 11.0506 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 87 HIS Chi-restraints excluded: chain G 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 132 ASP Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.179966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.154431 restraints weight = 11272.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.157933 restraints weight = 19663.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.157742 restraints weight = 8693.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.158218 restraints weight = 7046.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158510 restraints weight = 6276.695| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6019 Z= 0.199 Angle : 0.714 11.381 8483 Z= 0.387 Chirality : 0.041 0.230 956 Planarity : 0.004 0.031 802 Dihedral : 29.571 179.920 1494 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.31 % Allowed : 28.54 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.08 (0.35), residues: 516 helix: 1.70 (0.31), residues: 256 sheet: -0.61 (0.45), residues: 104 loop : 0.20 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 11 TYR 0.012 0.002 TYR N 76 PHE 0.018 0.002 PHE G 127 TRP 0.023 0.004 TRP M 107 HIS 0.007 0.001 HIS M 115 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5980) covalent geometry : angle 0.69432 ( 8465) hydrogen bonds : bond 0.04840 ( 298) hydrogen bonds : angle 3.97378 ( 792) metal coordination : bond 0.00394 ( 39) metal coordination : angle 3.71652 ( 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7289 (tm-30) cc_final: 0.7025 (tp-100) REVERT: M 51 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7126 (p) REVERT: M 65 ASP cc_start: 0.7213 (m-30) cc_final: 0.7002 (m-30) REVERT: M 104 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8000 (p) REVERT: N 14 ARG cc_start: 0.6133 (ttp80) cc_final: 0.5833 (tmm160) outliers start: 25 outliers final: 19 residues processed: 83 average time/residue: 0.0832 time to fit residues: 8.9473 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 50 THR 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 88 LEU 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 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS 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: 0.6980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS N 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.176851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.155662 restraints weight = 11185.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155420 restraints weight = 19822.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.155249 restraints weight = 9517.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.155494 restraints weight = 8479.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.155770 restraints weight = 6979.562| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 6019 Z= 0.271 Angle : 0.771 10.965 8483 Z= 0.417 Chirality : 0.043 0.179 956 Planarity : 0.005 0.054 802 Dihedral : 29.934 179.447 1494 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 7.32 % Allowed : 27.53 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.69 (0.35), residues: 516 helix: 1.46 (0.31), residues: 256 sheet: -0.98 (0.44), residues: 104 loop : 0.01 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 11 TYR 0.015 0.002 TYR N 76 PHE 0.018 0.003 PHE G 127 TRP 0.032 0.005 TRP H 107 HIS 0.010 0.002 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5980) covalent geometry : angle 0.74574 ( 8465) hydrogen bonds : bond 0.05330 ( 298) hydrogen bonds : angle 4.13920 ( 792) metal coordination : bond 0.02581 ( 39) metal coordination : angle 4.35020 ( 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 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7291 (tm-30) cc_final: 0.7064 (tp-100) REVERT: G 87 HIS cc_start: 0.5866 (OUTLIER) cc_final: 0.5201 (m90) REVERT: H 53 ARG cc_start: 0.8309 (ptp90) cc_final: 0.8043 (ptp90) REVERT: M 51 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7256 (p) REVERT: M 65 ASP cc_start: 0.7328 (m-30) cc_final: 0.6975 (m-30) REVERT: M 104 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8179 (p) REVERT: N 14 ARG cc_start: 0.6343 (ttp80) cc_final: 0.5997 (tmm160) outliers start: 29 outliers final: 23 residues processed: 90 average time/residue: 0.0891 time to fit residues: 9.9981 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 53 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 39 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 88 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4497 r_free = 0.4497 target = 0.177350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.156114 restraints weight = 11165.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.155874 restraints weight = 19097.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.155542 restraints weight = 9190.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155927 restraints weight = 7821.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.156043 restraints weight = 6580.916| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6019 Z= 0.203 Angle : 0.719 11.123 8483 Z= 0.390 Chirality : 0.040 0.151 956 Planarity : 0.004 0.037 802 Dihedral : 29.722 178.889 1494 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.82 % Allowed : 28.54 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.35), residues: 516 helix: 1.53 (0.31), residues: 256 sheet: -1.00 (0.44), residues: 104 loop : -0.02 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 11 TYR 0.014 0.002 TYR N 76 PHE 0.017 0.002 PHE G 127 TRP 0.030 0.004 TRP H 107 HIS 0.007 0.001 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 5980) covalent geometry : angle 0.69383 ( 8465) hydrogen bonds : bond 0.04618 ( 298) hydrogen bonds : angle 3.95041 ( 792) metal coordination : bond 0.00430 ( 39) metal coordination : angle 4.11239 ( 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7237 (tm-30) cc_final: 0.7028 (tp-100) REVERT: G 87 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5187 (m90) REVERT: H 53 ARG cc_start: 0.8242 (ptp90) cc_final: 0.8005 (ptp90) REVERT: M 51 VAL cc_start: 0.7547 (OUTLIER) cc_final: 0.7064 (p) REVERT: M 65 ASP cc_start: 0.7288 (m-30) cc_final: 0.7054 (m-30) REVERT: M 104 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7974 (p) REVERT: N 14 ARG cc_start: 0.6266 (ttp80) cc_final: 0.5919 (tmm160) outliers start: 27 outliers final: 20 residues processed: 84 average time/residue: 0.0738 time to fit residues: 8.0546 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 50 THR 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 88 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS 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: 10.0000 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4467 r_free = 0.4467 target = 0.174718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.152979 restraints weight = 11094.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.152627 restraints weight = 19978.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152164 restraints weight = 9712.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.152476 restraints weight = 8718.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152467 restraints weight = 7067.416| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6019 Z= 0.278 Angle : 0.791 10.695 8483 Z= 0.429 Chirality : 0.044 0.155 956 Planarity : 0.005 0.063 802 Dihedral : 30.188 179.982 1494 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 7.58 % Allowed : 27.53 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.35), residues: 516 helix: 1.22 (0.31), residues: 256 sheet: -1.19 (0.44), residues: 104 loop : -0.25 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 11 TYR 0.020 0.003 TYR N 76 PHE 0.018 0.003 PHE G 127 TRP 0.041 0.005 TRP H 107 HIS 0.011 0.002 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 5980) covalent geometry : angle 0.76207 ( 8465) hydrogen bonds : bond 0.05362 ( 298) hydrogen bonds : angle 4.26243 ( 792) metal coordination : bond 0.00630 ( 39) metal coordination : angle 4.69990 ( 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7242 (tm-30) cc_final: 0.7030 (tp-100) REVERT: G 87 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5472 (m90) REVERT: M 51 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7293 (p) REVERT: M 65 ASP cc_start: 0.7164 (m-30) cc_final: 0.6804 (m-30) REVERT: M 104 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8040 (p) REVERT: N 14 ARG cc_start: 0.6370 (ttp80) cc_final: 0.6037 (tmm160) outliers start: 30 outliers final: 22 residues processed: 83 average time/residue: 0.0765 time to fit residues: 8.1556 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 107 TRP 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 88 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 29 PHE 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 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.0000 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4512 r_free = 0.4512 target = 0.178571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.149140 restraints weight = 11385.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.153238 restraints weight = 18831.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.152875 restraints weight = 10298.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.153119 restraints weight = 9227.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.153674 restraints weight = 7521.035| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6019 Z= 0.174 Angle : 0.728 11.506 8483 Z= 0.390 Chirality : 0.040 0.203 956 Planarity : 0.004 0.026 802 Dihedral : 29.788 179.098 1494 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.81 % Allowed : 30.81 % Favored : 63.38 % 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: 0.67 (0.35), residues: 516 helix: 1.58 (0.31), residues: 256 sheet: -1.09 (0.44), residues: 104 loop : -0.18 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 53 TYR 0.013 0.002 TYR N 76 PHE 0.019 0.002 PHE G 127 TRP 0.030 0.003 TRP H 107 HIS 0.006 0.001 HIS N 84 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5980) covalent geometry : angle 0.70463 ( 8465) hydrogen bonds : bond 0.04056 ( 298) hydrogen bonds : angle 3.94520 ( 792) metal coordination : bond 0.00363 ( 39) metal coordination : angle 4.05563 ( 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5556 (m90) REVERT: M 51 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7178 (p) REVERT: M 104 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8030 (p) REVERT: N 14 ARG cc_start: 0.6352 (ttp80) cc_final: 0.5881 (tmm160) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.1037 time to fit residues: 11.1245 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 107 TRP 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 88 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 95 LYS Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.177469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.155634 restraints weight = 11060.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154795 restraints weight = 20531.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.154152 restraints weight = 11938.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.154815 restraints weight = 9481.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.154966 restraints weight = 7247.983| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6019 Z= 0.204 Angle : 0.748 11.004 8483 Z= 0.403 Chirality : 0.040 0.183 956 Planarity : 0.004 0.041 802 Dihedral : 29.915 178.975 1494 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.56 % Allowed : 30.30 % Favored : 64.14 % 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: 0.64 (0.35), residues: 516 helix: 1.58 (0.32), residues: 256 sheet: -1.11 (0.44), residues: 104 loop : -0.22 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 53 TYR 0.015 0.002 TYR N 76 PHE 0.018 0.002 PHE G 127 TRP 0.028 0.003 TRP H 107 HIS 0.007 0.001 HIS N 86 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5980) covalent geometry : angle 0.72467 ( 8465) hydrogen bonds : bond 0.04440 ( 298) hydrogen bonds : angle 3.97686 ( 792) metal coordination : bond 0.00438 ( 39) metal coordination : angle 4.04697 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1015.22 seconds wall clock time: 18 minutes 11.26 seconds (1091.26 seconds total)