Starting phenix.real_space_refine on Mon Mar 11 12:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv9_23530/03_2024/7lv9_23530.pdb" } resolution = 4.5 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= -0.000 sd= 1.006 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 P 190 5.49 5 S 26 5.16 5 C 4566 2.51 5 N 1515 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 680 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1931 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "H" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1964 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Time building chain proxies: 4.94, per 1000 atoms: 0.60 Number of scatterers: 8238 At special positions: 0 Unit cell: (71.94, 115.54, 118.81, 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 26 16.00 P 190 15.00 O 1941 8.00 N 1515 7.00 C 4566 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: 4.12 Conformation dependent library (CDL) restraints added in 987.5 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 64.7% alpha, 1.7% beta 88 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.570A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 74 removed outlier: 3.594A pdb=" N LEU B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.545A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'A' and resid 127 through 136 removed outlier: 3.525A pdb=" N VAL A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.848A pdb=" N GLU A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 3.586A pdb=" N ILE A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.717A pdb=" N ILE A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 35 through 61 Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.698A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 103 removed outlier: 3.547A pdb=" N GLY D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.771A pdb=" N ALA C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.546A pdb=" N ILE C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.734A pdb=" N ALA C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.660A pdb=" N LEU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 74 removed outlier: 3.675A pdb=" N LEU F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.554A pdb=" N VAL F 84 " --> pdb=" O MET F 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.511A pdb=" N VAL E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 158 removed outlier: 3.740A pdb=" N LYS E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 195 removed outlier: 3.502A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 211 removed outlier: 3.604A pdb=" N ILE E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.959A pdb=" N SER B 43 " --> pdb=" O VAL A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'D' and resid 33 through 34 removed outlier: 7.202A pdb=" N SER D 33 " --> pdb=" O ILE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AA5, first strand: chain 'F' and resid 78 through 79 255 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 228 hydrogen bonds 456 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1568 1.33 - 1.45: 2740 1.45 - 1.57: 4025 1.57 - 1.69: 378 1.69 - 1.81: 45 Bond restraints: 8756 Sorted by residual: bond pdb=" C3' DG H 20 " pdb=" O3' DG H 20 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.42e+00 bond pdb=" CB ASP B 47 " pdb=" CG ASP B 47 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.35e+00 bond pdb=" C3' DT H -59 " pdb=" O3' DT H -59 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" N GLY E 117 " pdb=" CA GLY E 117 " ideal model delta sigma weight residual 1.449 1.468 -0.019 1.45e-02 4.76e+03 1.64e+00 bond pdb=" CA ASP B 47 " pdb=" CB ASP B 47 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.51e-02 4.39e+03 1.58e+00 ... (remaining 8751 not shown) Histogram of bond angle deviations from ideal: 97.74 - 104.72: 752 104.72 - 111.70: 4681 111.70 - 118.68: 2459 118.68 - 125.66: 4081 125.66 - 132.64: 645 Bond angle restraints: 12618 Sorted by residual: angle pdb=" C3' DG H 20 " pdb=" O3' DG H 20 " pdb=" P DG H 21 " ideal model delta sigma weight residual 120.20 124.87 -4.67 1.50e+00 4.44e-01 9.67e+00 angle pdb=" CB ASP B 47 " pdb=" CG ASP B 47 " pdb=" OD1 ASP B 47 " ideal model delta sigma weight residual 118.40 124.93 -6.53 2.30e+00 1.89e-01 8.05e+00 angle pdb=" C ALA E 121 " pdb=" N GLY E 122 " pdb=" CA GLY E 122 " ideal model delta sigma weight residual 122.80 120.09 2.71 9.70e-01 1.06e+00 7.80e+00 angle pdb=" C GLU C 105 " pdb=" CA GLU C 105 " pdb=" CB GLU C 105 " ideal model delta sigma weight residual 110.10 115.36 -5.26 1.90e+00 2.77e-01 7.66e+00 angle pdb=" CB GLU E 178 " pdb=" CG GLU E 178 " pdb=" CD GLU E 178 " ideal model delta sigma weight residual 112.60 117.19 -4.59 1.70e+00 3.46e-01 7.30e+00 ... (remaining 12613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 3882 34.62 - 69.25: 891 69.25 - 103.87: 13 103.87 - 138.49: 0 138.49 - 173.11: 2 Dihedral angle restraints: 4788 sinusoidal: 3134 harmonic: 1654 Sorted by residual: dihedral pdb=" C4' DG H 20 " pdb=" C3' DG H 20 " pdb=" O3' DG H 20 " pdb=" P DG H 21 " ideal model delta sinusoidal sigma weight residual 220.00 46.89 173.11 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT H -59 " pdb=" C3' DT H -59 " pdb=" O3' DT H -59 " pdb=" P DC H -58 " ideal model delta sinusoidal sigma weight residual 220.00 76.28 143.72 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" N LYS B 62 " pdb=" CA LYS B 62 " pdb=" CB LYS B 62 " pdb=" CG LYS B 62 " ideal model delta sinusoidal sigma weight residual -60.00 -115.61 55.61 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1022 0.032 - 0.065: 334 0.065 - 0.097: 79 0.097 - 0.130: 25 0.130 - 0.162: 6 Chirality restraints: 1466 Sorted by residual: chirality pdb=" P DG H 21 " pdb=" OP1 DG H 21 " pdb=" OP2 DG H 21 " pdb=" O5' DG H 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ILE B 27 " pdb=" N ILE B 27 " pdb=" C ILE B 27 " pdb=" CB ILE B 27 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE A 143 " pdb=" N ILE A 143 " pdb=" C ILE A 143 " pdb=" CB ILE A 143 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1463 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 47 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ASP B 47 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP B 47 " -0.021 2.00e-02 2.50e+03 pdb=" N THR B 48 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 178 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU E 178 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU E 178 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU E 178 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC G 36 " -0.023 2.00e-02 2.50e+03 1.11e-02 2.80e+00 pdb=" N1 DC G 36 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DC G 36 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC G 36 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC G 36 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC G 36 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC G 36 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC G 36 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC G 36 " 0.005 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 3 2.05 - 2.76: 1153 2.76 - 3.47: 10281 3.47 - 4.19: 23108 4.19 - 4.90: 33128 Nonbonded interactions: 67673 Sorted by model distance: nonbonded pdb=" C LYS D 104 " pdb=" N GLU C 105 " model vdw 1.334 3.350 nonbonded pdb=" C SER B 112 " pdb=" N CYS A 113 " model vdw 1.335 3.350 nonbonded pdb=" C SER F 112 " pdb=" N CYS E 113 " model vdw 1.337 3.350 nonbonded pdb=" O LYS F 29 " pdb=" OG1 THR F 32 " model vdw 2.206 2.440 nonbonded pdb=" O LYS D 104 " pdb=" N GLU C 105 " model vdw 2.250 2.520 ... (remaining 67668 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 'A' and (resid 113 through 122 or (resid 123 and (name N or name CA or na \ me C or name O or name CB )) or resid 124 through 214)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } 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: 0.910 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: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 28.980 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 : 0.003 0.063 8756 Z= 0.194 Angle : 0.639 7.072 12618 Z= 0.385 Chirality : 0.036 0.162 1466 Planarity : 0.004 0.032 927 Dihedral : 27.068 173.114 3714 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.35 (0.25), residues: 569 helix: -2.29 (0.18), residues: 360 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 57 PHE 0.024 0.002 PHE C 152 TYR 0.024 0.003 TYR D 100 ARG 0.005 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.726 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: D 24 MET cc_start: 0.8435 (mtp) cc_final: 0.8220 (ttp) REVERT: E 151 MET cc_start: 0.8408 (mtp) cc_final: 0.7705 (mtt) REVERT: E 176 ILE cc_start: 0.9069 (mt) cc_final: 0.8434 (mt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2560 time to fit residues: 22.5308 Evaluate side-chains 32 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8756 Z= 0.350 Angle : 0.700 6.114 12618 Z= 0.417 Chirality : 0.038 0.171 1466 Planarity : 0.007 0.106 927 Dihedral : 30.621 177.558 2675 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.22 % Allowed : 3.47 % Favored : 96.31 % 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: 0.55 (0.33), residues: 569 helix: 1.43 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 131 PHE 0.029 0.003 PHE F 96 TYR 0.015 0.002 TYR D 81 ARG 0.007 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.871 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: D 24 MET cc_start: 0.8922 (mtp) cc_final: 0.8549 (ttm) REVERT: D 93 MET cc_start: 0.8815 (mtm) cc_final: 0.8261 (ttp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2650 time to fit residues: 15.0090 Evaluate side-chains 30 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN F 57 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8756 Z= 0.268 Angle : 0.639 5.765 12618 Z= 0.384 Chirality : 0.035 0.146 1466 Planarity : 0.005 0.093 927 Dihedral : 31.208 177.744 2675 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.43 % Allowed : 3.25 % Favored : 96.31 % 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: 1.44 (0.33), residues: 569 helix: 2.14 (0.25), residues: 356 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 88 PHE 0.018 0.002 PHE C 152 TYR 0.021 0.002 TYR D 81 ARG 0.007 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8858 (mtp) cc_final: 0.8539 (ttm) REVERT: D 93 MET cc_start: 0.8746 (mtm) cc_final: 0.8307 (ptm) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.2312 time to fit residues: 12.1036 Evaluate side-chains 30 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8756 Z= 0.213 Angle : 0.579 6.918 12618 Z= 0.349 Chirality : 0.034 0.202 1466 Planarity : 0.003 0.027 927 Dihedral : 31.197 178.350 2675 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 1.87 (0.34), residues: 569 helix: 2.44 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 88 PHE 0.018 0.001 PHE C 152 TYR 0.014 0.001 TYR D 81 ARG 0.003 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 MET cc_start: 0.8770 (mtm) cc_final: 0.8322 (ptm) REVERT: E 151 MET cc_start: 0.8586 (mtt) cc_final: 0.8057 (mmt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2112 time to fit residues: 10.5762 Evaluate side-chains 27 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8756 Z= 0.335 Angle : 0.706 11.048 12618 Z= 0.414 Chirality : 0.038 0.159 1466 Planarity : 0.005 0.061 927 Dihedral : 31.892 174.414 2675 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 1.46 (0.34), residues: 569 helix: 2.01 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 164 PHE 0.023 0.003 PHE C 152 TYR 0.009 0.002 TYR D 81 ARG 0.014 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.9199 (mt) cc_final: 0.8958 (mt) REVERT: D 93 MET cc_start: 0.8775 (mtm) cc_final: 0.8468 (ptm) REVERT: E 151 MET cc_start: 0.8437 (mtt) cc_final: 0.8178 (mtt) REVERT: E 210 MET cc_start: 0.7418 (tpt) cc_final: 0.7011 (tpt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2242 time to fit residues: 9.7570 Evaluate side-chains 27 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8756 Z= 0.349 Angle : 0.716 7.516 12618 Z= 0.423 Chirality : 0.039 0.218 1466 Planarity : 0.005 0.039 927 Dihedral : 32.733 175.874 2675 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 0.67 (0.33), residues: 569 helix: 1.23 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS B 57 PHE 0.013 0.002 PHE C 152 TYR 0.010 0.002 TYR C 151 ARG 0.013 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.9197 (mt) cc_final: 0.8961 (mt) REVERT: D 93 MET cc_start: 0.8853 (mtm) cc_final: 0.8519 (ptm) REVERT: E 210 MET cc_start: 0.7575 (tpt) cc_final: 0.7176 (tpt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2079 time to fit residues: 8.6989 Evaluate side-chains 24 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.8210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8756 Z= 0.246 Angle : 0.638 6.791 12618 Z= 0.379 Chirality : 0.036 0.177 1466 Planarity : 0.003 0.023 927 Dihedral : 32.563 176.120 2675 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.33 (0.34), residues: 569 helix: 1.76 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 164 PHE 0.010 0.002 PHE C 152 TYR 0.006 0.001 TYR D 100 ARG 0.007 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.9239 (mt) cc_final: 0.9022 (mt) REVERT: D 93 MET cc_start: 0.8777 (mtm) cc_final: 0.8340 (mtm) REVERT: E 210 MET cc_start: 0.7454 (tpt) cc_final: 0.7035 (tpt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2042 time to fit residues: 8.8539 Evaluate side-chains 27 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8756 Z= 0.210 Angle : 0.607 7.164 12618 Z= 0.363 Chirality : 0.036 0.175 1466 Planarity : 0.003 0.025 927 Dihedral : 32.475 175.476 2675 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.59 (0.35), residues: 569 helix: 2.01 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.87 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 164 PHE 0.011 0.001 PHE C 152 TYR 0.005 0.001 TYR D 100 ARG 0.004 0.001 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.9236 (mt) cc_final: 0.9033 (mt) REVERT: D 93 MET cc_start: 0.8779 (mtm) cc_final: 0.8337 (mtm) REVERT: E 210 MET cc_start: 0.7416 (tpt) cc_final: 0.6993 (tpt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2132 time to fit residues: 9.1694 Evaluate side-chains 28 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8756 Z= 0.189 Angle : 0.595 7.059 12618 Z= 0.356 Chirality : 0.035 0.165 1466 Planarity : 0.003 0.025 927 Dihedral : 32.314 176.115 2675 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.35), residues: 569 helix: 2.23 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.78 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 92 PHE 0.010 0.001 PHE C 152 TYR 0.005 0.001 TYR D 81 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: D 24 MET cc_start: 0.8192 (ppp) cc_final: 0.7858 (ppp) REVERT: D 93 MET cc_start: 0.8798 (mtm) cc_final: 0.8362 (mtm) REVERT: E 210 MET cc_start: 0.7455 (tpt) cc_final: 0.7020 (tpt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2277 time to fit residues: 9.8177 Evaluate side-chains 26 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 61 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.8766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8756 Z= 0.284 Angle : 0.648 11.954 12618 Z= 0.385 Chirality : 0.036 0.146 1466 Planarity : 0.004 0.031 927 Dihedral : 32.512 176.177 2675 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.52 (0.34), residues: 569 helix: 1.91 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.81 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 34 PHE 0.013 0.002 PHE C 152 TYR 0.008 0.001 TYR D 100 ARG 0.005 0.001 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 93 MET cc_start: 0.8803 (mtm) cc_final: 0.8364 (mtm) REVERT: E 210 MET cc_start: 0.7528 (tpt) cc_final: 0.7104 (tpt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2297 time to fit residues: 9.7163 Evaluate side-chains 26 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.0470 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.0570 chunk 41 optimal weight: 10.0000 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** 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 = 0.2642 r_free = 0.2642 target = 0.023139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.017434 restraints weight = 158958.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.017909 restraints weight = 100707.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.018267 restraints weight = 76289.882| |-----------------------------------------------------------------------------| r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8756 Z= 0.177 Angle : 0.595 12.076 12618 Z= 0.352 Chirality : 0.035 0.128 1466 Planarity : 0.003 0.025 927 Dihedral : 32.229 176.992 2675 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.35), residues: 569 helix: 2.28 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 29 PHE 0.011 0.001 PHE C 152 TYR 0.005 0.001 TYR D 81 ARG 0.006 0.000 ARG E 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.24 seconds wall clock time: 24 minutes 32.71 seconds (1472.71 seconds total)