Starting phenix.real_space_refine on Thu Jul 24 07:30:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049.map" model { file = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/07_2025/7vo9_32049_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 86 5.49 5 S 24 5.16 5 C 3247 2.51 5 N 1066 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5711 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2419 SG CYS G 90 17.241 31.300 59.728 1.00 71.88 S ATOM 2441 SG CYS G 93 14.793 30.618 62.671 1.00 70.47 S ATOM 2714 SG CYS G 130 14.935 28.682 59.367 1.00 73.41 S ATOM 2733 SG CYS G 133 13.753 32.726 60.427 1.00 76.67 S ATOM 2333 SG CYS G 79 25.843 20.667 68.382 1.00 55.29 S ATOM 3403 SG CYS H 90 50.589 21.848 55.123 1.00 65.50 S ATOM 3425 SG CYS H 93 53.560 23.049 52.848 1.00 67.51 S ATOM 3698 SG CYS H 130 51.610 19.758 52.799 1.00 70.00 S ATOM 3717 SG CYS H 133 54.743 21.183 55.225 1.00 77.21 S ATOM 3317 SG CYS H 79 41.604 31.101 44.386 1.00 60.89 S ATOM 4387 SG CYS M 90 18.888 56.432 98.247 1.00 65.11 S ATOM 4409 SG CYS M 93 16.467 57.794 95.462 1.00 65.03 S ATOM 4682 SG CYS M 130 15.148 58.615 98.647 1.00 66.03 S ATOM 4701 SG CYS M 133 15.423 55.317 97.309 1.00 76.02 S ATOM 4301 SG CYS M 79 28.244 66.312 88.717 1.00 55.78 S ATOM 5371 SG CYS N 90 52.577 62.137 102.734 1.00 63.37 S ATOM 5393 SG CYS N 93 56.120 61.109 103.694 1.00 66.66 S ATOM 5666 SG CYS N 130 54.023 63.902 105.638 1.00 70.51 S ATOM 5285 SG CYS N 79 41.722 54.410 113.951 1.00 42.33 S Time building chain proxies: 4.15, per 1000 atoms: 0.73 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: 1.23 Conformation dependent library (CDL) restraints added in 608.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " Number of angles added : 18 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 48.9% alpha, 17.9% beta 31 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'G' and resid 13 through 26 Processing helix chain 'G' and resid 31 through 43 Processing helix chain 'G' and resid 47 through 62 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.724A pdb=" N GLU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 116 removed outlier: 3.882A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'M' and resid 13 through 26 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 3.614A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 Processing sheet with id=AA1, first strand: chain 'G' and resid 65 through 68 Processing sheet with id=AA2, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.678A pdb=" N LYS G 95 " --> pdb=" O CYS G 90 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR G 117 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS H 130 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN G 119 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY H 128 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA G 121 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE H 126 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR G 123 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL H 124 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU G 125 " --> pdb=" O HIS H 122 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N HIS H 122 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE G 127 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL H 120 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR G 129 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AA5, first strand: chain 'M' and resid 64 through 68 Processing sheet with id=AA6, first strand: chain 'M' and resid 96 through 99 removed outlier: 6.098A pdb=" N HIS M 87 " --> pdb=" O ILE M 126 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY M 128 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL M 89 " --> pdb=" O GLY M 128 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN N 119 " --> pdb=" O THR M 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AA8, first strand: chain 'N' and resid 95 through 99 220 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.48 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: 1.380 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.34), residues: 516 helix: 3.25 (0.28), residues: 256 sheet: 0.71 (0.51), residues: 88 loop : 0.54 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 107 HIS 0.040 0.003 HIS G 122 PHE 0.014 0.003 PHE G 29 TYR 0.016 0.003 TYR G 117 ARG 0.005 0.001 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.20605 ( 298) hydrogen bonds : angle 7.18813 ( 792) metal coordination : bond 0.21004 ( 39) metal coordination : angle 15.68208 ( 18) covalent geometry : bond 0.01124 ( 5980) covalent geometry : angle 1.58019 ( 8465) *********************** 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 : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 111 ILE cc_start: 0.7594 (pt) cc_final: 0.6963 (pt) REVERT: N 52 TYR cc_start: 0.7282 (m-80) cc_final: 0.6971 (m-80) REVERT: N 99 VAL cc_start: 0.8508 (m) cc_final: 0.8074 (t) outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.3023 time to fit residues: 56.7699 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 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 = 0.4579 r_free = 0.4579 target = 0.185540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.157247 restraints weight = 11417.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.161256 restraints weight = 18103.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.161817 restraints weight = 9680.297| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6019 Z= 0.212 Angle : 0.752 9.210 8483 Z= 0.417 Chirality : 0.042 0.151 956 Planarity : 0.004 0.042 802 Dihedral : 27.506 178.883 1494 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 3.79 % Allowed : 20.45 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.34), residues: 516 helix: 2.75 (0.29), residues: 256 sheet: 0.61 (0.47), residues: 96 loop : 0.17 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 107 HIS 0.007 0.002 HIS N 86 PHE 0.017 0.003 PHE G 127 TYR 0.010 0.001 TYR H 117 ARG 0.006 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 298) hydrogen bonds : angle 4.07853 ( 792) metal coordination : bond 0.00721 ( 39) metal coordination : angle 5.52813 ( 18) covalent geometry : bond 0.00478 ( 5980) covalent geometry : angle 0.70836 ( 8465) *********************** 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 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 126 ILE cc_start: 0.8107 (tp) cc_final: 0.7900 (pt) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.2182 time to fit residues: 24.4885 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 HIS ** 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 = 0.4526 r_free = 0.4526 target = 0.180123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.153284 restraints weight = 11194.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156259 restraints weight = 20489.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.156593 restraints weight = 10495.953| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5153 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= 0.237 Angle : 0.755 9.019 8483 Z= 0.408 Chirality : 0.043 0.136 956 Planarity : 0.004 0.038 802 Dihedral : 28.649 177.255 1494 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.06 % Allowed : 20.20 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.35), residues: 516 helix: 2.24 (0.30), residues: 256 sheet: -0.13 (0.46), residues: 104 loop : 0.36 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP M 107 HIS 0.009 0.002 HIS N 86 PHE 0.016 0.002 PHE G 127 TYR 0.015 0.002 TYR N 117 ARG 0.005 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 298) hydrogen bonds : angle 4.15106 ( 792) metal coordination : bond 0.00634 ( 39) metal coordination : angle 5.24458 ( 18) covalent geometry : bond 0.00549 ( 5980) covalent geometry : angle 0.71639 ( 8465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 HIS cc_start: 0.5725 (OUTLIER) cc_final: 0.5423 (m90) REVERT: H 48 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8595 (tt) REVERT: H 56 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6793 (mt0) outliers start: 24 outliers final: 15 residues processed: 83 average time/residue: 0.2468 time to fit residues: 24.9573 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 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 48 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 66 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 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** ** 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 = 0.4491 r_free = 0.4491 target = 0.177310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.156013 restraints weight = 11318.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155655 restraints weight = 18663.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.155729 restraints weight = 9480.940| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6019 Z= 0.228 Angle : 0.733 10.520 8483 Z= 0.400 Chirality : 0.042 0.160 956 Planarity : 0.004 0.039 802 Dihedral : 29.118 178.940 1494 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 7.07 % Allowed : 23.23 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.35), residues: 516 helix: 1.96 (0.30), residues: 256 sheet: -0.35 (0.46), residues: 104 loop : 0.31 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP M 107 HIS 0.009 0.001 HIS N 86 PHE 0.017 0.002 PHE G 127 TYR 0.011 0.002 TYR N 76 ARG 0.005 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 298) hydrogen bonds : angle 4.12172 ( 792) metal coordination : bond 0.00623 ( 39) metal coordination : angle 4.58002 ( 18) covalent geometry : bond 0.00524 ( 5980) covalent geometry : angle 0.70273 ( 8465) *********************** 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 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6931 (tp-100) REVERT: G 87 HIS cc_start: 0.5576 (OUTLIER) cc_final: 0.5051 (m90) REVERT: H 30 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6993 (mmm-85) REVERT: H 56 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7029 (pt0) REVERT: M 51 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7406 (p) REVERT: M 65 ASP cc_start: 0.7066 (m-30) cc_final: 0.6781 (m-30) REVERT: M 104 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8245 (p) outliers start: 28 outliers final: 19 residues processed: 90 average time/residue: 0.2317 time to fit residues: 25.5938 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 : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 50 THR 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 38 MET 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 50 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.179371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.159710 restraints weight = 11175.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.157228 restraints weight = 19253.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.155942 restraints weight = 12227.361| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6019 Z= 0.201 Angle : 0.723 10.871 8483 Z= 0.393 Chirality : 0.040 0.137 956 Planarity : 0.004 0.031 802 Dihedral : 29.439 178.040 1494 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.57 % Allowed : 27.02 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 516 helix: 1.83 (0.30), residues: 256 sheet: -0.44 (0.46), residues: 104 loop : 0.21 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP M 107 HIS 0.007 0.001 HIS N 86 PHE 0.017 0.002 PHE G 127 TYR 0.013 0.002 TYR N 117 ARG 0.007 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 298) hydrogen bonds : angle 4.02397 ( 792) metal coordination : bond 0.00424 ( 39) metal coordination : angle 4.34343 ( 18) covalent geometry : bond 0.00465 ( 5980) covalent geometry : angle 0.69542 ( 8465) *********************** 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: 26 poor density : 72 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7308 (tm-30) cc_final: 0.7041 (tp-100) REVERT: G 87 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.5285 (m90) REVERT: H 56 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: M 65 ASP cc_start: 0.7383 (m-30) cc_final: 0.7023 (m-30) REVERT: M 104 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8185 (p) outliers start: 26 outliers final: 19 residues processed: 88 average time/residue: 0.1916 time to fit residues: 21.4757 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 87 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 56 GLN 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.0060 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.181826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.153652 restraints weight = 11221.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.155388 restraints weight = 17672.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.156918 restraints weight = 10247.897| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6019 Z= 0.172 Angle : 0.684 10.913 8483 Z= 0.377 Chirality : 0.039 0.146 956 Planarity : 0.003 0.023 802 Dihedral : 29.438 179.015 1494 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.56 % Allowed : 27.53 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.35), residues: 516 helix: 1.92 (0.31), residues: 256 sheet: -0.51 (0.46), residues: 104 loop : 0.18 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP M 107 HIS 0.006 0.001 HIS M 115 PHE 0.016 0.002 PHE G 127 TYR 0.011 0.002 TYR N 76 ARG 0.007 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 298) hydrogen bonds : angle 3.86642 ( 792) metal coordination : bond 0.00307 ( 39) metal coordination : angle 3.66697 ( 18) covalent geometry : bond 0.00397 ( 5980) covalent geometry : angle 0.66327 ( 8465) *********************** 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 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7294 (tm-30) cc_final: 0.7052 (tp-100) REVERT: G 87 HIS cc_start: 0.5815 (OUTLIER) cc_final: 0.5285 (m90) REVERT: H 56 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: M 51 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7285 (p) REVERT: M 65 ASP cc_start: 0.7199 (m-30) cc_final: 0.6916 (m-30) REVERT: M 104 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8259 (p) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.2200 time to fit residues: 25.0107 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 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 50 THR Chi-restraints excluded: chain H residue 56 GLN 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 99 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.180487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.153634 restraints weight = 11398.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154831 restraints weight = 20921.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.155829 restraints weight = 12126.600| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6019 Z= 0.167 Angle : 0.683 11.152 8483 Z= 0.372 Chirality : 0.038 0.149 956 Planarity : 0.003 0.018 802 Dihedral : 29.535 178.817 1494 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 6.57 % Allowed : 27.78 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 516 helix: 1.87 (0.31), residues: 256 sheet: -0.73 (0.44), residues: 104 loop : 0.12 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP H 107 HIS 0.005 0.001 HIS N 84 PHE 0.018 0.002 PHE G 127 TYR 0.010 0.002 TYR N 76 ARG 0.006 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 298) hydrogen bonds : angle 3.81492 ( 792) metal coordination : bond 0.00300 ( 39) metal coordination : angle 3.37482 ( 18) covalent geometry : bond 0.00385 ( 5980) covalent geometry : angle 0.66599 ( 8465) *********************** 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: 26 poor density : 72 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.7305 (tm-30) cc_final: 0.7086 (tp-100) REVERT: G 87 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5124 (m90) REVERT: H 56 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: M 51 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7160 (p) REVERT: M 65 ASP cc_start: 0.7168 (m-30) cc_final: 0.6901 (m-30) REVERT: M 104 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8140 (p) outliers start: 26 outliers final: 18 residues processed: 90 average time/residue: 0.1878 time to fit residues: 21.4638 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL 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 50 THR 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 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 51 VAL Chi-restraints excluded: chain N residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.177376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.157063 restraints weight = 11083.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.156234 restraints weight = 18589.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.155702 restraints weight = 9737.703| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.7309 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= 0.210 Angle : 0.737 11.288 8483 Z= 0.395 Chirality : 0.041 0.155 956 Planarity : 0.004 0.043 802 Dihedral : 29.807 178.936 1494 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 7.07 % Allowed : 28.28 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.35), residues: 516 helix: 1.68 (0.31), residues: 256 sheet: -0.77 (0.45), residues: 104 loop : 0.08 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP N 107 HIS 0.008 0.001 HIS N 86 PHE 0.017 0.002 PHE G 127 TYR 0.015 0.003 TYR N 76 ARG 0.005 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 298) hydrogen bonds : angle 3.96237 ( 792) metal coordination : bond 0.00534 ( 39) metal coordination : angle 4.39598 ( 18) covalent geometry : bond 0.00485 ( 5980) covalent geometry : angle 0.70978 ( 8465) *********************** 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: 28 poor density : 65 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: H 56 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: M 51 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7137 (p) REVERT: M 65 ASP cc_start: 0.7288 (m-30) cc_final: 0.7052 (m-30) REVERT: M 104 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (p) outliers start: 28 outliers final: 21 residues processed: 83 average time/residue: 0.1773 time to fit residues: 19.1010 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 50 THR 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 H residue 126 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 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 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 130 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.177560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.150574 restraints weight = 11108.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.153203 restraints weight = 19910.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.153737 restraints weight = 9329.090| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 6019 Z= 0.226 Angle : 0.755 11.158 8483 Z= 0.401 Chirality : 0.040 0.157 956 Planarity : 0.004 0.036 802 Dihedral : 29.770 179.031 1494 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.57 % Allowed : 29.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.35), residues: 516 helix: 1.69 (0.31), residues: 256 sheet: -0.86 (0.45), residues: 104 loop : -0.04 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP H 107 HIS 0.007 0.001 HIS N 86 PHE 0.018 0.003 PHE G 127 TYR 0.014 0.002 TYR N 76 ARG 0.006 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 298) hydrogen bonds : angle 3.89309 ( 792) metal coordination : bond 0.03720 ( 39) metal coordination : angle 4.40267 ( 18) covalent geometry : bond 0.00470 ( 5980) covalent geometry : angle 0.72778 ( 8465) *********************** 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: 26 poor density : 66 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 51 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7158 (p) REVERT: M 65 ASP cc_start: 0.7338 (m-30) cc_final: 0.7079 (m-30) REVERT: M 104 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (p) outliers start: 26 outliers final: 20 residues processed: 82 average time/residue: 0.1991 time to fit residues: 20.8603 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 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 75 VAL Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 89 VAL 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 21 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.180140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.152744 restraints weight = 11391.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.155968 restraints weight = 20425.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.156133 restraints weight = 10787.461| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6019 Z= 0.167 Angle : 0.711 10.100 8483 Z= 0.381 Chirality : 0.038 0.150 956 Planarity : 0.003 0.028 802 Dihedral : 29.625 179.746 1494 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.55 % Allowed : 31.06 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 516 helix: 1.90 (0.31), residues: 256 sheet: -1.03 (0.44), residues: 104 loop : -0.10 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP H 107 HIS 0.006 0.001 HIS N 84 PHE 0.019 0.002 PHE G 127 TYR 0.014 0.002 TYR H 76 ARG 0.006 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 298) hydrogen bonds : angle 3.74282 ( 792) metal coordination : bond 0.00426 ( 39) metal coordination : angle 3.95436 ( 18) covalent geometry : bond 0.00387 ( 5980) covalent geometry : angle 0.68783 ( 8465) ********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 87 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.5226 (m90) REVERT: H 56 GLN cc_start: 0.6887 (pt0) cc_final: 0.6614 (pt0) REVERT: M 51 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7122 (p) REVERT: M 65 ASP cc_start: 0.7114 (m-30) cc_final: 0.6864 (m-30) outliers start: 18 outliers final: 14 residues processed: 84 average time/residue: 0.2008 time to fit residues: 21.2791 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain G residue 87 HIS 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 132 ASP 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 130 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 57 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.181676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.162216 restraints weight = 11353.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.160920 restraints weight = 18443.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.160150 restraints weight = 11643.635| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6019 Z= 0.163 Angle : 0.705 9.923 8483 Z= 0.377 Chirality : 0.038 0.217 956 Planarity : 0.003 0.043 802 Dihedral : 29.617 179.549 1494 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.79 % Allowed : 31.57 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 516 helix: 1.91 (0.32), residues: 256 sheet: -0.96 (0.44), residues: 104 loop : -0.14 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP N 107 HIS 0.005 0.001 HIS N 84 PHE 0.019 0.002 PHE G 127 TYR 0.009 0.002 TYR N 76 ARG 0.006 0.001 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 298) hydrogen bonds : angle 3.73577 ( 792) metal coordination : bond 0.00308 ( 39) metal coordination : angle 3.68142 ( 18) covalent geometry : bond 0.00377 ( 5980) covalent geometry : angle 0.68485 ( 8465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.51 seconds wall clock time: 34 minutes 56.80 seconds (2096.80 seconds total)