Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:42:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vo9_32049/04_2023/7vo9_32049_neut.pdb" } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 86 5.49 5 S 24 5.16 5 C 3247 2.51 5 N 1066 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 27": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.05, per 1000 atoms: 0.71 Number of scatterers: 5711 At special positions: 0 Unit cell: (73.7, 90.2, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 24 16.00 P 86 15.00 O 1276 8.00 N 1066 7.00 C 3247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 612.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " Number of angles added : 18 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 48.9% alpha, 17.9% beta 31 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.88 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: 1.63 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1007 1.33 - 1.45: 1909 1.45 - 1.58: 2866 1.58 - 1.70: 170 1.70 - 1.82: 28 Bond restraints: 5980 Sorted by residual: bond pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.32e+01 bond pdb=" N VAL M 89 " pdb=" CA VAL M 89 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N ILE N 126 " pdb=" CA ILE N 126 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N VAL M 64 " pdb=" CA VAL M 64 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N VAL N 64 " pdb=" CA VAL N 64 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.22e-02 6.72e+03 1.09e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.46: 767 107.46 - 114.20: 3203 114.20 - 120.93: 2515 120.93 - 127.67: 1815 127.67 - 134.40: 165 Bond angle restraints: 8465 Sorted by residual: angle pdb=" C4' DT A 33 " pdb=" C3' DT A 33 " pdb=" O3' DT A 33 " ideal model delta sigma weight residual 110.00 118.05 -8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" O3' DT B 82 " pdb=" C3' DT B 82 " pdb=" C2' DT B 82 " ideal model delta sigma weight residual 111.50 119.05 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CA HIS M 86 " pdb=" CB HIS M 86 " pdb=" CG HIS M 86 " ideal model delta sigma weight residual 113.80 109.06 4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" N GLY G 94 " pdb=" CA GLY G 94 " pdb=" C GLY G 94 " ideal model delta sigma weight residual 115.30 108.81 6.49 1.39e+00 5.18e-01 2.18e+01 angle pdb=" N GLY M 94 " pdb=" CA GLY M 94 " pdb=" C GLY M 94 " ideal model delta sigma weight residual 115.36 109.19 6.17 1.33e+00 5.65e-01 2.15e+01 ... (remaining 8460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 2960 35.05 - 70.09: 263 70.09 - 105.13: 2 105.13 - 140.18: 7 140.18 - 175.22: 6 Dihedral angle restraints: 3238 sinusoidal: 1746 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 3235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 645 0.083 - 0.165: 255 0.165 - 0.248: 50 0.248 - 0.330: 3 0.330 - 0.412: 3 Chirality restraints: 956 Sorted by residual: chirality pdb=" C3' DT B 82 " pdb=" C4' DT B 82 " pdb=" O3' DT B 82 " pdb=" C2' DT B 82 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C3' DG B 56 " pdb=" C4' DG B 56 " pdb=" O3' DG B 56 " pdb=" C2' DG B 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ASP N 60 " pdb=" N ASP N 60 " pdb=" C ASP N 60 " pdb=" CB ASP N 60 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 953 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 122 " 0.011 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG HIS G 122 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS G 122 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS G 122 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS G 122 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS G 122 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS M 86 " -0.019 2.00e-02 2.50e+03 1.93e-02 5.56e+00 pdb=" CG HIS M 86 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS M 86 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS M 86 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 72 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C GLY M 72 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY M 72 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU M 73 " 0.012 2.00e-02 2.50e+03 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 179 2.68 - 3.23: 4633 3.23 - 3.79: 10248 3.79 - 4.34: 13092 4.34 - 4.90: 18444 Nonbonded interactions: 46596 Sorted by model distance: nonbonded pdb=" OD2 ASP H 65 " pdb="ZN ZN H 202 " model vdw 2.124 2.230 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.230 2.230 nonbonded pdb=" C2' DG B 42 " pdb=" O5' DT B 43 " model vdw 2.332 3.440 nonbonded pdb=" C2' DT B 71 " pdb=" N7 DG B 72 " model vdw 2.439 3.520 nonbonded pdb=" O ILE M 111 " pdb=" ND1 HIS M 115 " model vdw 2.496 2.520 ... (remaining 46591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 5.690 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.044 5980 Z= 0.732 Angle : 1.580 8.054 8465 Z= 1.205 Chirality : 0.088 0.412 956 Planarity : 0.004 0.027 802 Dihedral : 23.082 175.224 2278 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 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 0.533 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 outliers start: 3 outliers final: 0 residues processed: 162 average time/residue: 0.3267 time to fit residues: 61.1842 Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 HIS M 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 5980 Z= 0.289 Angle : 0.711 8.049 8465 Z= 0.417 Chirality : 0.042 0.144 956 Planarity : 0.005 0.043 802 Dihedral : 27.843 179.373 1422 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer Outliers : 4.55 % 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: 2.35 (0.34), residues: 516 helix: 2.83 (0.30), residues: 256 sheet: 0.31 (0.45), residues: 104 loop : 0.34 (0.45), residues: 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 96 average time/residue: 0.2652 time to fit residues: 30.6560 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0652 time to fit residues: 1.3008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5980 Z= 0.250 Angle : 0.661 9.407 8465 Z= 0.381 Chirality : 0.040 0.132 956 Planarity : 0.004 0.023 802 Dihedral : 28.795 177.363 1422 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer Outliers : 4.29 % 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: 2.05 (0.35), residues: 516 helix: 2.57 (0.30), residues: 256 sheet: 0.07 (0.45), residues: 104 loop : 0.32 (0.46), residues: 156 *********************** 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 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.2542 time to fit residues: 26.5493 Evaluate side-chains 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0571 time to fit residues: 1.8555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 5980 Z= 0.247 Angle : 0.662 10.001 8465 Z= 0.376 Chirality : 0.040 0.171 956 Planarity : 0.004 0.029 802 Dihedral : 29.098 178.157 1422 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 3.79 % 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: 1.57 (0.35), residues: 516 helix: 2.05 (0.31), residues: 256 sheet: -0.16 (0.46), residues: 104 loop : 0.35 (0.46), residues: 156 *********************** 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 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 0.2515 time to fit residues: 25.4509 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0587 time to fit residues: 1.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 5980 Z= 0.270 Angle : 0.684 10.124 8465 Z= 0.389 Chirality : 0.040 0.150 956 Planarity : 0.004 0.031 802 Dihedral : 29.414 179.141 1422 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.02 % 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: 1.35 (0.35), residues: 516 helix: 1.81 (0.31), residues: 256 sheet: -0.32 (0.46), residues: 104 loop : 0.43 (0.48), residues: 156 *********************** 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 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.2533 time to fit residues: 21.9963 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0536 time to fit residues: 1.1628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 5980 Z= 0.305 Angle : 0.706 10.465 8465 Z= 0.395 Chirality : 0.041 0.136 956 Planarity : 0.004 0.042 802 Dihedral : 29.857 179.632 1422 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.78 % 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: 1.03 (0.35), residues: 516 helix: 1.59 (0.31), residues: 256 sheet: -0.65 (0.45), residues: 104 loop : 0.33 (0.48), residues: 156 *********************** 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 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.2474 time to fit residues: 21.9243 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0900 time to fit residues: 1.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 5980 Z= 0.263 Angle : 0.675 10.603 8465 Z= 0.381 Chirality : 0.040 0.200 956 Planarity : 0.004 0.027 802 Dihedral : 29.957 179.206 1422 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.77 % 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: 1.09 (0.35), residues: 516 helix: 1.69 (0.31), residues: 256 sheet: -0.68 (0.45), residues: 104 loop : 0.31 (0.48), residues: 156 *********************** 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 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.2461 time to fit residues: 20.6518 Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0658 time to fit residues: 1.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 5980 Z= 0.362 Angle : 0.754 10.601 8465 Z= 0.416 Chirality : 0.043 0.155 956 Planarity : 0.005 0.050 802 Dihedral : 30.435 178.586 1422 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 2.02 % 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: 0.62 (0.35), residues: 516 helix: 1.33 (0.30), residues: 256 sheet: -0.95 (0.43), residues: 104 loop : 0.09 (0.48), residues: 156 *********************** 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 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.2184 time to fit residues: 19.2999 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1051 time to fit residues: 1.7244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5980 Z= 0.223 Angle : 0.669 11.279 8465 Z= 0.372 Chirality : 0.038 0.140 956 Planarity : 0.003 0.034 802 Dihedral : 29.931 179.859 1422 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.52 % 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: 1.75 (0.31), residues: 256 sheet: -0.94 (0.42), residues: 104 loop : 0.16 (0.47), residues: 156 *********************** 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 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.2502 time to fit residues: 21.7744 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0883 time to fit residues: 1.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 5980 Z= 0.366 Angle : 0.758 12.069 8465 Z= 0.419 Chirality : 0.043 0.158 956 Planarity : 0.005 0.046 802 Dihedral : 30.325 179.237 1422 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 0.76 % 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: 0.59 (0.35), residues: 516 helix: 1.35 (0.31), residues: 256 sheet: -1.01 (0.43), residues: 104 loop : 0.02 (0.47), residues: 156 ********************** 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 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.2491 time to fit residues: 19.9430 Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1946 time to fit residues: 1.1224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 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 = 0.4524 r_free = 0.4524 target = 0.179736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.159657 restraints weight = 11080.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.157374 restraints weight = 18349.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.156099 restraints weight = 11941.049| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 5980 Z= 0.258 Angle : 0.693 10.240 8465 Z= 0.385 Chirality : 0.039 0.208 956 Planarity : 0.004 0.038 802 Dihedral : 30.093 179.487 1422 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.35), residues: 516 helix: 1.58 (0.31), residues: 256 sheet: -1.01 (0.44), residues: 104 loop : 0.01 (0.47), residues: 156 =============================================================================== Job complete usr+sys time: 1395.72 seconds wall clock time: 25 minutes 52.23 seconds (1552.23 seconds total)