Starting phenix.real_space_refine on Fri Mar 15 19:02:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zms_11300/03_2024/6zms_11300.pdb" } resolution = 3.4 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= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 4031 2.51 5 N 1087 2.21 5 O 1228 1.98 5 H 6173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4236 Classifications: {'peptide': 271} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "B" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3782 Classifications: {'peptide': 252} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3661 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 223} Chain: "D" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 891 Inner-chain residues flagged as termini: ['pdbres="GLY D 10 "', 'pdbres="ALA D 11 "'] Classifications: {'peptide': 57} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 2 Time building chain proxies: 5.78, per 1000 atoms: 0.46 Number of scatterers: 12570 At special positions: 0 Unit cell: (90.52, 71.92, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1228 8.00 N 1087 7.00 C 4031 6.00 H 6173 1.00 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: 10.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 5.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.604A pdb=" N LEU A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.549A pdb=" N LYS A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.526A pdb=" N TRP A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 155 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 178 through 182 removed outlier: 3.550A pdb=" N LEU B 182 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.546A pdb=" N TYR C 68 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 144 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.796A pdb=" N CYS C 212 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 71 removed outlier: 5.654A pdb=" N CYS A 64 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 231 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 66 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 7.309A pdb=" N VAL A 240 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 104 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 238 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 238 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.537A pdb=" N VAL B 32 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.537A pdb=" N VAL B 32 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 239 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.783A pdb=" N PHE B 219 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 121 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN B 119 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 105 removed outlier: 4.676A pdb=" N HIS B 99 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B 254 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 101 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 252 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ARG B 103 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 250 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 86 removed outlier: 7.492A pdb=" N GLN C 81 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR C 194 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 83 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.208A pdb=" N TYR C 107 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 225 " --> pdb=" O TYR C 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 141 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 6154 1.13 - 1.31: 1052 1.31 - 1.48: 2756 1.48 - 1.65: 2685 1.65 - 1.83: 83 Bond restraints: 12730 Sorted by residual: bond pdb=" N ILE D 23 " pdb=" H ILE D 23 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" CE1 HIS A 117 " pdb=" HE1 HIS A 117 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" CE1 HIS B 118 " pdb=" HE1 HIS B 118 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CE1 HIS B 99 " pdb=" HE1 HIS B 99 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CE1 HIS A 43 " pdb=" HE1 HIS A 43 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 12725 not shown) Histogram of bond angle deviations from ideal: 94.73 - 102.55: 102 102.55 - 110.37: 10477 110.37 - 118.19: 6222 118.19 - 126.01: 5946 126.01 - 133.83: 136 Bond angle restraints: 22883 Sorted by residual: angle pdb=" N ILE C 103 " pdb=" CA ILE C 103 " pdb=" C ILE C 103 " ideal model delta sigma weight residual 113.20 104.17 9.03 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N PHE D 52 " pdb=" CA PHE D 52 " pdb=" C PHE D 52 " ideal model delta sigma weight residual 114.31 105.72 8.59 1.29e+00 6.01e-01 4.43e+01 angle pdb=" CA PRO A 139 " pdb=" C PRO A 139 " pdb=" O PRO A 139 " ideal model delta sigma weight residual 120.90 116.18 4.72 7.20e-01 1.93e+00 4.29e+01 angle pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" C GLU A 26 " ideal model delta sigma weight residual 112.94 103.92 9.02 1.41e+00 5.03e-01 4.09e+01 angle pdb=" CA PHE C 118 " pdb=" CB PHE C 118 " pdb=" CG PHE C 118 " ideal model delta sigma weight residual 113.80 107.51 6.29 1.00e+00 1.00e+00 3.96e+01 ... (remaining 22878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5680 17.95 - 35.90: 208 35.90 - 53.85: 90 53.85 - 71.81: 132 71.81 - 89.76: 10 Dihedral angle restraints: 6120 sinusoidal: 3273 harmonic: 2847 Sorted by residual: dihedral pdb=" CA VAL A 255 " pdb=" C VAL A 255 " pdb=" N ASN A 256 " pdb=" CA ASN A 256 " ideal model delta harmonic sigma weight residual 180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ILE A 66 " pdb=" C ILE A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ALA D 11 " pdb=" C ALA D 11 " pdb=" N HIS D 12 " pdb=" CA HIS D 12 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 719 0.098 - 0.196: 230 0.196 - 0.294: 28 0.294 - 0.391: 7 0.391 - 0.489: 3 Chirality restraints: 987 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA THR A 155 " pdb=" N THR A 155 " pdb=" C THR A 155 " pdb=" CB THR A 155 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA GLN C 27 " pdb=" N GLN C 27 " pdb=" C GLN C 27 " pdb=" CB GLN C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 984 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 12 " -0.161 2.00e-02 2.50e+03 8.34e-02 1.57e+02 pdb=" CG HIS D 12 " 0.131 2.00e-02 2.50e+03 pdb=" ND1 HIS D 12 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 HIS D 12 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS D 12 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS D 12 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 HIS D 12 " 0.038 2.00e-02 2.50e+03 pdb=" HD2 HIS D 12 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS D 12 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 153 " -0.136 2.00e-02 2.50e+03 5.82e-02 1.35e+02 pdb=" CG TRP A 153 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 153 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 153 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 153 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP A 153 " 0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 153 " 0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 153 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 153 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 153 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP A 153 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 TRP A 153 " 0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP A 153 " 0.066 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 153 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 153 " -0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 153 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 185 " 0.154 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG TYR B 185 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 185 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR B 185 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR B 185 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 185 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR B 185 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 185 " 0.135 2.00e-02 2.50e+03 pdb=" HD1 TYR B 185 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR B 185 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR B 185 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR B 185 " -0.010 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.95: 119 1.95 - 2.61: 13096 2.61 - 3.27: 37617 3.27 - 3.94: 50623 3.94 - 4.60: 76602 Nonbonded interactions: 178057 Sorted by model distance: nonbonded pdb=" H LYS D 51 " pdb=" H PHE D 52 " model vdw 1.283 2.100 nonbonded pdb=" H ALA C 91 " pdb=" H SER C 92 " model vdw 1.363 2.100 nonbonded pdb=" H ALA A 73 " pdb=" H GLU A 74 " model vdw 1.399 2.100 nonbonded pdb=" H ALA C 139 " pdb=" H GLY C 140 " model vdw 1.407 2.100 nonbonded pdb=" H MET C 78 " pdb=" H GLY C 79 " model vdw 1.413 2.100 ... (remaining 178052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.340 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: 0.200 Extract box with map and model: 13.430 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 43.050 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 : 0.019 0.061 6557 Z= 1.238 Angle : 1.985 9.499 8935 Z= 1.332 Chirality : 0.098 0.489 987 Planarity : 0.014 0.097 1163 Dihedral : 14.128 89.757 2360 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 2.98 % Allowed : 5.58 % Favored : 91.44 % Rotamer: Outliers : 2.12 % Allowed : 3.95 % Favored : 93.94 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 2.13 % 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: -2.88 (0.24), residues: 806 helix: -4.10 (0.49), residues: 51 sheet: -1.39 (0.31), residues: 219 loop : -2.00 (0.21), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.019 TRP A 153 HIS 0.008 0.002 HIS B 99 PHE 0.042 0.010 PHE C 120 TYR 0.144 0.020 TYR B 185 ARG 0.006 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 270 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6715 (ttp-170) REVERT: A 226 THR cc_start: 0.7709 (t) cc_final: 0.7464 (t) REVERT: B 195 ASN cc_start: 0.7484 (p0) cc_final: 0.7271 (p0) REVERT: C 149 MET cc_start: 0.6419 (pp-130) cc_final: 0.6133 (pp-130) REVERT: D 7 GLN cc_start: 0.5299 (mt0) cc_final: 0.4731 (mm-40) outliers start: 15 outliers final: 7 residues processed: 277 average time/residue: 0.3368 time to fit residues: 127.8198 Evaluate side-chains 211 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 125 ASN A 131 GLN A 154 GLN B 30 ASN B 119 GLN B 206 ASN C 20 GLN C 27 GLN C 35 ASN C 42 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6557 Z= 0.400 Angle : 0.786 7.170 8935 Z= 0.429 Chirality : 0.050 0.187 987 Planarity : 0.006 0.049 1163 Dihedral : 7.983 79.593 903 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.09 % Favored : 94.42 % Rotamer: Outliers : 3.53 % Allowed : 13.12 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.43 (0.25), residues: 806 helix: -4.58 (0.39), residues: 53 sheet: -0.45 (0.36), residues: 196 loop : -1.86 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 80 HIS 0.006 0.002 HIS A 214 PHE 0.013 0.002 PHE C 118 TYR 0.035 0.002 TYR A 67 ARG 0.005 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.062 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: A 152 VAL cc_start: 0.7148 (t) cc_final: 0.6892 (t) REVERT: A 171 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.7141 (ptt-90) REVERT: A 260 GLU cc_start: 0.6438 (mt-10) cc_final: 0.5894 (mt-10) REVERT: B 50 GLU cc_start: 0.4650 (pm20) cc_final: 0.3925 (pm20) REVERT: B 256 ARG cc_start: 0.6711 (pmt-80) cc_final: 0.5073 (mtt-85) REVERT: D 7 GLN cc_start: 0.7477 (mt0) cc_final: 0.6139 (mm-40) REVERT: D 8 LYS cc_start: 0.7818 (tptt) cc_final: 0.6851 (mtpt) outliers start: 25 outliers final: 14 residues processed: 229 average time/residue: 0.3504 time to fit residues: 106.9337 Evaluate side-chains 213 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6557 Z= 0.178 Angle : 0.554 4.683 8935 Z= 0.299 Chirality : 0.044 0.149 987 Planarity : 0.005 0.039 1163 Dihedral : 6.446 84.460 896 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.20 % Favored : 93.30 % Rotamer: Outliers : 2.40 % Allowed : 16.93 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.07 (0.26), residues: 806 helix: -4.42 (0.42), residues: 52 sheet: -0.11 (0.36), residues: 208 loop : -1.66 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 80 HIS 0.003 0.001 HIS C 109 PHE 0.011 0.001 PHE C 120 TYR 0.019 0.001 TYR A 67 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.5900 (OUTLIER) cc_final: 0.5686 (p0) REVERT: A 171 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.7131 (ptt-90) REVERT: A 260 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6109 (mt-10) REVERT: B 16 ILE cc_start: 0.8486 (mm) cc_final: 0.8174 (mm) REVERT: B 256 ARG cc_start: 0.6925 (pmt-80) cc_final: 0.5391 (mtt180) REVERT: D 7 GLN cc_start: 0.7585 (mt0) cc_final: 0.6208 (mm-40) REVERT: D 8 LYS cc_start: 0.7834 (tptt) cc_final: 0.7141 (mtpt) outliers start: 17 outliers final: 14 residues processed: 203 average time/residue: 0.3748 time to fit residues: 103.1704 Evaluate side-chains 191 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN C 35 ASN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6557 Z= 0.224 Angle : 0.547 4.919 8935 Z= 0.291 Chirality : 0.044 0.158 987 Planarity : 0.004 0.040 1163 Dihedral : 6.013 86.850 896 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.08 % Favored : 93.55 % Rotamer: Outliers : 3.53 % Allowed : 14.53 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.98 (0.27), residues: 806 helix: -4.15 (0.45), residues: 50 sheet: -0.01 (0.37), residues: 203 loop : -1.64 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.010 0.001 PHE A 257 TYR 0.020 0.001 TYR A 67 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6330 (mm-30) REVERT: A 260 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6177 (mt-10) REVERT: B 12 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7256 (mmm-85) REVERT: B 16 ILE cc_start: 0.8586 (mm) cc_final: 0.8363 (mm) REVERT: B 256 ARG cc_start: 0.7589 (pmt-80) cc_final: 0.5993 (mtt180) REVERT: D 8 LYS cc_start: 0.8220 (tptt) cc_final: 0.7392 (mtpt) outliers start: 25 outliers final: 21 residues processed: 194 average time/residue: 0.3067 time to fit residues: 80.0107 Evaluate side-chains 196 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.7618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6557 Z= 0.277 Angle : 0.544 7.690 8935 Z= 0.288 Chirality : 0.044 0.156 987 Planarity : 0.004 0.042 1163 Dihedral : 5.769 84.204 896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.20 % Favored : 93.42 % Rotamer: Outliers : 3.39 % Allowed : 16.22 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.99 (0.27), residues: 806 helix: -4.03 (0.49), residues: 50 sheet: -0.11 (0.36), residues: 219 loop : -1.66 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.013 0.001 PHE A 257 TYR 0.015 0.001 TYR A 67 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6103 (mt-10) REVERT: B 14 ARG cc_start: 0.5618 (tpt170) cc_final: 0.5370 (tpt170) REVERT: B 16 ILE cc_start: 0.8528 (mm) cc_final: 0.8301 (mm) REVERT: B 185 TYR cc_start: 0.8370 (m-80) cc_final: 0.7996 (m-80) REVERT: C 125 MET cc_start: 0.7253 (mmm) cc_final: 0.7048 (mmm) REVERT: C 210 ILE cc_start: 0.8537 (mm) cc_final: 0.8329 (mt) REVERT: D 8 LYS cc_start: 0.8358 (tptt) cc_final: 0.7457 (mtmt) outliers start: 24 outliers final: 17 residues processed: 190 average time/residue: 0.3377 time to fit residues: 87.2187 Evaluate side-chains 169 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.8261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6557 Z= 0.390 Angle : 0.563 4.335 8935 Z= 0.302 Chirality : 0.045 0.157 987 Planarity : 0.005 0.043 1163 Dihedral : 5.915 89.766 896 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.95 % Favored : 92.68 % Rotamer: Outliers : 3.53 % Allowed : 16.78 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.09 (0.27), residues: 806 helix: -4.01 (0.50), residues: 50 sheet: -0.08 (0.36), residues: 216 loop : -1.79 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.018 0.001 TYR A 67 ARG 0.005 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6319 (mm-30) REVERT: A 260 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6158 (mt-10) REVERT: C 203 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6108 (mm-30) REVERT: D 8 LYS cc_start: 0.8714 (tptt) cc_final: 0.7639 (mtmt) outliers start: 25 outliers final: 20 residues processed: 161 average time/residue: 0.3553 time to fit residues: 76.3264 Evaluate side-chains 164 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 41 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.8523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6557 Z= 0.289 Angle : 0.538 7.422 8935 Z= 0.282 Chirality : 0.043 0.148 987 Planarity : 0.004 0.042 1163 Dihedral : 5.758 89.490 896 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.20 % Favored : 93.42 % Rotamer: Outliers : 2.68 % Allowed : 18.76 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.27), residues: 806 helix: -4.05 (0.48), residues: 50 sheet: 0.05 (0.38), residues: 200 loop : -1.75 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.016 0.001 TYR A 67 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5998 (mt-10) REVERT: D 8 LYS cc_start: 0.8785 (tptt) cc_final: 0.7789 (mttt) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.3384 time to fit residues: 74.3481 Evaluate side-chains 157 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 0.0270 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.8588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6557 Z= 0.130 Angle : 0.509 8.745 8935 Z= 0.260 Chirality : 0.043 0.146 987 Planarity : 0.004 0.036 1163 Dihedral : 5.424 86.940 896 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.21 % Favored : 94.42 % Rotamer: Outliers : 1.41 % Allowed : 20.03 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.83 (0.27), residues: 806 helix: -3.93 (0.51), residues: 50 sheet: 0.15 (0.36), residues: 216 loop : -1.62 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.004 0.001 HIS A 214 PHE 0.009 0.001 PHE A 257 TYR 0.015 0.001 TYR A 67 ARG 0.004 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7380 (mm-40) REVERT: A 260 GLU cc_start: 0.6423 (mt-10) cc_final: 0.6218 (mt-10) REVERT: D 8 LYS cc_start: 0.8766 (tptt) cc_final: 0.7779 (mttt) outliers start: 10 outliers final: 9 residues processed: 161 average time/residue: 0.3568 time to fit residues: 77.9018 Evaluate side-chains 156 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 234 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6557 Z= 0.254 Angle : 0.538 9.554 8935 Z= 0.276 Chirality : 0.043 0.137 987 Planarity : 0.004 0.039 1163 Dihedral : 5.248 88.729 894 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.07 % Favored : 92.56 % Rotamer: Outliers : 2.26 % Allowed : 19.18 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.97 (0.27), residues: 806 helix: -4.06 (0.45), residues: 56 sheet: 0.22 (0.38), residues: 195 loop : -1.69 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.016 0.001 PHE A 257 TYR 0.013 0.001 TYR C 194 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6216 (mt-10) REVERT: D 8 LYS cc_start: 0.8836 (tptt) cc_final: 0.7760 (mttt) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.3535 time to fit residues: 74.3583 Evaluate side-chains 153 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain D residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 79 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 67 optimal weight: 0.1980 chunk 19 optimal weight: 10.0000 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6557 Z= 0.137 Angle : 0.515 10.700 8935 Z= 0.259 Chirality : 0.043 0.150 987 Planarity : 0.004 0.037 1163 Dihedral : 4.999 86.521 894 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.09 % Favored : 95.53 % Rotamer: Outliers : 1.27 % Allowed : 20.31 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.67 (0.27), residues: 806 helix: -3.72 (0.53), residues: 49 sheet: 0.29 (0.36), residues: 216 loop : -1.54 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 80 HIS 0.003 0.001 HIS A 214 PHE 0.014 0.001 PHE A 257 TYR 0.016 0.001 TYR A 67 ARG 0.005 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6167 (mt-10) REVERT: B 14 ARG cc_start: 0.4971 (tpt170) cc_final: 0.4726 (tpt170) REVERT: D 8 LYS cc_start: 0.8795 (tptt) cc_final: 0.7738 (mttt) outliers start: 9 outliers final: 8 residues processed: 157 average time/residue: 0.3532 time to fit residues: 74.2488 Evaluate side-chains 153 residues out of total 709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 187 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.077564 restraints weight = 33582.364| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.77 r_work: 0.2662 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.8912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6557 Z= 0.208 Angle : 0.525 10.041 8935 Z= 0.267 Chirality : 0.043 0.138 987 Planarity : 0.004 0.038 1163 Dihedral : 5.005 87.943 894 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.08 % Favored : 93.55 % Rotamer: Outliers : 1.55 % Allowed : 19.89 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.70 (0.27), residues: 806 helix: -3.73 (0.51), residues: 49 sheet: 0.28 (0.36), residues: 216 loop : -1.57 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.012 0.001 TYR A 67 ARG 0.004 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.18 seconds wall clock time: 65 minutes 4.42 seconds (3904.42 seconds total)