Starting phenix.real_space_refine on Thu Jul 2 09:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_23530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_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/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_23530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_23530.map" model { file = "/net/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_23530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lv9_23530/07_2026/7lv9_23530.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'HIS:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASP: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: 1.85, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " CYS A 113 " - " SER B 112 " " GLU C 105 " - " LYS D 104 " " CYS E 113 " - " SER F 112 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 325.5 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: 1.08 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: 1.55 Time building geometry restraints manager: 0.90 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 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" C5' DA G 57 " pdb=" C4' DA G 57 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.38e+01 bond pdb=" C3' DG H -37 " pdb=" C2' DG H -37 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DG H 23 " pdb=" C2' DG H 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC H 11 " pdb=" C2' DC H 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 ... (remaining 8751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11556 1.41 - 2.83: 986 2.83 - 4.24: 58 4.24 - 5.66: 13 5.66 - 7.07: 5 Bond angle restraints: 12618 Sorted by residual: angle pdb=" O4' DG G 47 " pdb=" C4' DG G 47 " pdb=" C3' DG G 47 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+01 angle pdb=" O5' DA G 57 " pdb=" C5' DA G 57 " pdb=" C4' DA G 57 " ideal model delta sigma weight residual 109.40 113.09 -3.69 8.00e-01 1.56e+00 2.12e+01 angle pdb=" N3 DT G -17 " pdb=" C4 DT G -17 " pdb=" O4 DT G -17 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT G -28 " pdb=" C4 DT G -28 " pdb=" O4 DT G -28 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT G 12 " pdb=" C4 DT G 12 " pdb=" O4 DT G 12 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 12613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 3891 34.62 - 69.25: 891 69.25 - 103.87: 13 103.87 - 138.49: 0 138.49 - 173.11: 2 Dihedral angle restraints: 4797 sinusoidal: 3140 harmonic: 1657 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 4794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 900 0.037 - 0.074: 416 0.074 - 0.111: 137 0.111 - 0.148: 9 0.148 - 0.186: 4 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C3' DT H -59 " pdb=" C4' DT H -59 " pdb=" O3' DT H -59 " pdb=" C2' DT H -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" C3' DG H 20 " pdb=" C4' DG H 20 " pdb=" O3' DG H 20 " pdb=" C2' DG H 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.04e-01 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 2.34 -2.51 -0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 1463 not shown) Planarity restraints: 930 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 927 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 732 2.74 - 3.28: 7081 3.28 - 3.82: 15741 3.82 - 4.36: 18073 4.36 - 4.90: 26034 Nonbonded interactions: 67661 Sorted by model distance: nonbonded pdb=" O LYS F 29 " pdb=" OG1 THR F 32 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" OP2 DA H -14 " model vdw 2.333 3.040 nonbonded pdb=" O LEU F 42 " pdb=" ND2 ASN E 128 " model vdw 2.336 3.120 nonbonded pdb=" OE2 GLU D 37 " pdb=" OG SER F 108 " model vdw 2.350 3.040 nonbonded pdb=" NZ LYS B 75 " pdb=" OP2 DG H -33 " model vdw 2.370 3.120 ... (remaining 67656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- 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 : 0.006 0.050 8759 Z= 0.538 Angle : 0.791 7.072 12627 Z= 0.686 Chirality : 0.045 0.186 1466 Planarity : 0.004 0.032 927 Dihedral : 27.068 173.114 3714 Min Nonbonded Distance : 2.206 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.000 ARG C 129 TYR 0.024 0.003 TYR D 100 PHE 0.024 0.002 PHE C 152 HIS 0.003 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.54 ( 8756) covalent geometry : angle 0.79111 / 0.69 (12618) hydrogen bonds : bond 0.20477 / 14.05 ( 483) hydrogen bonds : angle 5.61629 / 4.06 ( 1221) link_TRANS : bond 0.00674 / 0.34 ( 3) link_TRANS : angle 0.80364 / 0.41 ( 9) *********************** 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 to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.144 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: 0.8219 (ttp) REVERT: E 151 MET cc_start: 0.8408 (mtp) cc_final: 0.7706 (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: 0.1057 time to fit residues: 9.3504 Evaluate side-chains 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN C 118 GLN E 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.027868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.021161 restraints weight = 152390.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.021673 restraints weight = 100468.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.022071 restraints weight = 76199.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.022344 restraints weight = 63316.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.022536 restraints weight = 55840.822| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 8759 Z= 0.357 Angle : 0.944 9.686 12627 Z= 0.527 Chirality : 0.050 0.308 1466 Planarity : 0.008 0.103 927 Dihedral : 31.113 178.373 2675 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 569 helix: 0.67 (0.24), residues: 359 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG E 114 TYR 0.012 0.003 TYR D 100 PHE 0.036 0.004 PHE C 152 HIS 0.014 0.003 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.36 ( 8756) covalent geometry : angle 0.94473 / 0.53 (12618) hydrogen bonds : bond 0.12358 / 8.40 ( 483) hydrogen bonds : angle 3.80394 / 2.73 ( 1221) link_TRANS : bond 0.00256 / 0.13 ( 3) link_TRANS : angle 0.39697 / 0.20 ( 9) *********************** 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 to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9685 (tmm) cc_final: 0.9455 (tmm) REVERT: B 80 MET cc_start: 0.8119 (mtp) cc_final: 0.7817 (mmm) REVERT: A 172 MET cc_start: 0.8189 (ptt) cc_final: 0.7913 (ppp) REVERT: D 93 MET cc_start: 0.9560 (mtm) cc_final: 0.9133 (ptm) REVERT: C 153 MET cc_start: 0.9242 (mmt) cc_final: 0.8712 (mmm) REVERT: F 91 MET cc_start: 0.9007 (mmp) cc_final: 0.8785 (mmm) REVERT: E 151 MET cc_start: 0.9476 (mtp) cc_final: 0.9232 (mtt) REVERT: E 172 MET cc_start: 0.9784 (tpt) cc_final: 0.9458 (mmm) REVERT: E 210 MET cc_start: 0.9636 (ttp) cc_final: 0.9302 (tpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0950 time to fit residues: 5.3748 Evaluate side-chains 28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 50.0000 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.027114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.020863 restraints weight = 152918.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.021342 restraints weight = 101181.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.021718 restraints weight = 77351.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.021916 restraints weight = 64348.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022140 restraints weight = 57613.018| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8759 Z= 0.223 Angle : 0.693 7.354 12627 Z= 0.413 Chirality : 0.044 0.414 1466 Planarity : 0.005 0.049 927 Dihedral : 31.488 179.640 2675 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.22 % Allowed : 1.95 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.33), residues: 569 helix: 1.84 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 76 TYR 0.019 0.002 TYR D 81 PHE 0.022 0.002 PHE C 152 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.22 ( 8756) covalent geometry : angle 0.69353 / 0.41 (12618) hydrogen bonds : bond 0.06766 / 4.68 ( 483) hydrogen bonds : angle 3.30696 / 2.31 ( 1221) link_TRANS : bond 0.00147 / 0.07 ( 3) link_TRANS : angle 0.21119 / 0.13 ( 9) *********************** 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 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.219 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: B 58 MET cc_start: 0.9750 (tmm) cc_final: 0.9527 (tmm) REVERT: A 172 MET cc_start: 0.8447 (ptt) cc_final: 0.8072 (ppp) REVERT: A 173 LEU cc_start: 0.9857 (tp) cc_final: 0.9526 (mt) REVERT: D 93 MET cc_start: 0.9599 (mtm) cc_final: 0.9175 (ptm) REVERT: C 153 MET cc_start: 0.9487 (mmt) cc_final: 0.8870 (mmp) REVERT: F 91 MET cc_start: 0.9111 (mmp) cc_final: 0.8859 (mmm) REVERT: E 151 MET cc_start: 0.9426 (mtp) cc_final: 0.9179 (mtt) REVERT: E 172 MET cc_start: 0.9769 (tpt) cc_final: 0.9494 (mmt) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.0734 time to fit residues: 3.8607 Evaluate side-chains 30 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.027554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.021188 restraints weight = 151536.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.021735 restraints weight = 97418.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.022156 restraints weight = 73319.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022444 restraints weight = 60313.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.022640 restraints weight = 52435.006| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8759 Z= 0.157 Angle : 0.628 9.097 12627 Z= 0.374 Chirality : 0.042 0.396 1466 Planarity : 0.004 0.046 927 Dihedral : 31.421 178.778 2675 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 569 helix: 2.31 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -1.21 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 76 TYR 0.016 0.002 TYR D 81 PHE 0.019 0.002 PHE C 152 HIS 0.002 0.001 HIS F 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.16 ( 8756) covalent geometry : angle 0.62796 / 0.37 (12618) hydrogen bonds : bond 0.05262 / 3.62 ( 483) hydrogen bonds : angle 3.12561 / 2.15 ( 1221) link_TRANS : bond 0.00077 / 0.04 ( 3) link_TRANS : angle 0.14668 / 0.08 ( 9) *********************** 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 34 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9751 (tmm) cc_final: 0.9542 (tmm) REVERT: B 80 MET cc_start: 0.9058 (mmp) cc_final: 0.8847 (mtt) REVERT: A 172 MET cc_start: 0.8512 (ptt) cc_final: 0.8220 (ppp) REVERT: A 173 LEU cc_start: 0.9846 (tp) cc_final: 0.9520 (mt) REVERT: D 24 MET cc_start: 0.9492 (ttm) cc_final: 0.9082 (ttm) REVERT: C 153 MET cc_start: 0.9408 (mmt) cc_final: 0.8757 (mmp) REVERT: F 91 MET cc_start: 0.9074 (mmp) cc_final: 0.8815 (mmm) REVERT: E 151 MET cc_start: 0.9485 (mtp) cc_final: 0.9232 (mtt) REVERT: E 172 MET cc_start: 0.9760 (tpt) cc_final: 0.9505 (mmm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0711 time to fit residues: 3.5634 Evaluate side-chains 27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.0040 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.026746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.020487 restraints weight = 155472.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.021002 restraints weight = 101335.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.021399 restraints weight = 76614.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.021608 restraints weight = 63416.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.021830 restraints weight = 56397.633| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8759 Z= 0.169 Angle : 0.632 7.787 12627 Z= 0.375 Chirality : 0.042 0.414 1466 Planarity : 0.004 0.041 927 Dihedral : 31.460 179.348 2675 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.22 % Allowed : 1.30 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.35), residues: 569 helix: 2.55 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -1.19 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 76 TYR 0.015 0.002 TYR D 81 PHE 0.017 0.002 PHE C 152 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.17 ( 8756) covalent geometry : angle 0.63186 / 0.37 (12618) hydrogen bonds : bond 0.05664 / 3.91 ( 483) hydrogen bonds : angle 3.07912 / 2.13 ( 1221) link_TRANS : bond 0.00115 / 0.05 ( 3) link_TRANS : angle 0.13957 / 0.07 ( 9) *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9754 (tmm) cc_final: 0.9542 (tmm) REVERT: B 80 MET cc_start: 0.9054 (mmp) cc_final: 0.8284 (mmm) REVERT: A 172 MET cc_start: 0.8543 (ptt) cc_final: 0.8236 (ppp) REVERT: A 173 LEU cc_start: 0.9858 (tp) cc_final: 0.9567 (mt) REVERT: D 24 MET cc_start: 0.9385 (ttm) cc_final: 0.9095 (ttm) REVERT: D 93 MET cc_start: 0.9542 (mtm) cc_final: 0.9205 (ttp) REVERT: C 153 MET cc_start: 0.9431 (mmt) cc_final: 0.8774 (mmp) REVERT: F 80 MET cc_start: 0.8583 (pmm) cc_final: 0.8241 (pmm) REVERT: F 91 MET cc_start: 0.9128 (mmp) cc_final: 0.8860 (mmm) REVERT: E 136 MET cc_start: 0.9566 (ttm) cc_final: 0.9351 (tmm) REVERT: E 151 MET cc_start: 0.9484 (mtp) cc_final: 0.9239 (mtt) REVERT: E 172 MET cc_start: 0.9772 (tpt) cc_final: 0.9522 (mmt) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0789 time to fit residues: 3.8710 Evaluate side-chains 27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.025195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.019208 restraints weight = 163134.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.019707 restraints weight = 106998.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.019996 restraints weight = 81308.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.020290 restraints weight = 68268.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.020426 restraints weight = 60001.343| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8759 Z= 0.205 Angle : 0.701 10.071 12627 Z= 0.408 Chirality : 0.044 0.429 1466 Planarity : 0.006 0.094 927 Dihedral : 31.792 177.373 2675 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.34), residues: 569 helix: 2.11 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 199 TYR 0.024 0.002 TYR D 81 PHE 0.020 0.002 PHE C 152 HIS 0.006 0.002 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.21 ( 8756) covalent geometry : angle 0.70135 / 0.41 (12618) hydrogen bonds : bond 0.07573 / 5.21 ( 483) hydrogen bonds : angle 3.26544 / 2.25 ( 1221) link_TRANS : bond 0.00184 / 0.09 ( 3) link_TRANS : angle 0.27158 / 0.11 ( 9) *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9750 (tmm) cc_final: 0.9332 (ppp) REVERT: B 80 MET cc_start: 0.9141 (mmp) cc_final: 0.8390 (mmm) REVERT: D 24 MET cc_start: 0.9427 (ttm) cc_final: 0.9064 (ttm) REVERT: D 93 MET cc_start: 0.9582 (mtm) cc_final: 0.9210 (ptm) REVERT: C 153 MET cc_start: 0.9477 (mmt) cc_final: 0.8895 (ptt) REVERT: F 80 MET cc_start: 0.8886 (pmm) cc_final: 0.8482 (pmm) REVERT: F 91 MET cc_start: 0.9139 (mmp) cc_final: 0.8899 (mmm) REVERT: E 172 MET cc_start: 0.9743 (tpt) cc_final: 0.9515 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0653 time to fit residues: 3.1061 Evaluate side-chains 27 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 30.0000 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.0010 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 overall best weight: 2.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.026053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.019931 restraints weight = 157405.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.020545 restraints weight = 98308.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.020953 restraints weight = 72425.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.021227 restraints weight = 58843.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.021378 restraints weight = 51097.140| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8759 Z= 0.142 Angle : 0.614 9.016 12627 Z= 0.365 Chirality : 0.043 0.413 1466 Planarity : 0.003 0.040 927 Dihedral : 31.778 176.878 2675 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.35), residues: 569 helix: 2.48 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.80 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.012 0.001 TYR D 81 PHE 0.013 0.001 PHE C 152 HIS 0.003 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.14 ( 8756) covalent geometry : angle 0.61395 / 0.36 (12618) hydrogen bonds : bond 0.04588 / 3.20 ( 483) hydrogen bonds : angle 3.09351 / 2.12 ( 1221) link_TRANS : bond 0.00074 / 0.04 ( 3) link_TRANS : angle 0.15685 / 0.09 ( 9) *********************** 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 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9724 (tmm) cc_final: 0.9510 (tmm) REVERT: B 80 MET cc_start: 0.9022 (mmp) cc_final: 0.8251 (mmm) REVERT: A 172 MET cc_start: 0.9186 (ppp) cc_final: 0.8872 (ppp) REVERT: A 173 LEU cc_start: 0.9808 (mt) cc_final: 0.9561 (mt) REVERT: D 93 MET cc_start: 0.9579 (mtm) cc_final: 0.9167 (ptm) REVERT: C 153 MET cc_start: 0.9478 (mmt) cc_final: 0.8804 (mmp) REVERT: F 80 MET cc_start: 0.8730 (pmm) cc_final: 0.8313 (pmm) REVERT: F 91 MET cc_start: 0.9080 (mmp) cc_final: 0.8867 (mmm) REVERT: E 210 MET cc_start: 0.8619 (tpt) cc_final: 0.8297 (tpt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0913 time to fit residues: 4.3651 Evaluate side-chains 28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 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 = 0.2725 r_free = 0.2725 target = 0.024832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.018920 restraints weight = 163443.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.019420 restraints weight = 107645.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.019777 restraints weight = 81894.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.019996 restraints weight = 68214.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.020112 restraints weight = 60325.518| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8759 Z= 0.198 Angle : 0.670 7.672 12627 Z= 0.391 Chirality : 0.043 0.412 1466 Planarity : 0.004 0.062 927 Dihedral : 31.879 175.551 2675 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.34), residues: 569 helix: 2.22 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 133 TYR 0.011 0.001 TYR D 81 PHE 0.027 0.002 PHE D 48 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.20 ( 8756) covalent geometry : angle 0.67003 / 0.39 (12618) hydrogen bonds : bond 0.07182 / 4.95 ( 483) hydrogen bonds : angle 3.24755 / 2.26 ( 1221) link_TRANS : bond 0.00182 / 0.09 ( 3) link_TRANS : angle 0.24476 / 0.12 ( 9) *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9737 (tmm) cc_final: 0.9524 (tmm) REVERT: B 80 MET cc_start: 0.9138 (mmp) cc_final: 0.8399 (mmm) REVERT: D 93 MET cc_start: 0.9583 (mtm) cc_final: 0.9200 (ptm) REVERT: C 153 MET cc_start: 0.9542 (mmt) cc_final: 0.8878 (mmp) REVERT: F 80 MET cc_start: 0.8841 (pmm) cc_final: 0.8413 (pmm) REVERT: F 91 MET cc_start: 0.9138 (mmp) cc_final: 0.8909 (mmm) REVERT: E 171 ASP cc_start: 0.9533 (m-30) cc_final: 0.9308 (m-30) REVERT: E 172 MET cc_start: 0.9393 (mmt) cc_final: 0.8909 (mmm) REVERT: E 210 MET cc_start: 0.8679 (tpt) cc_final: 0.8358 (tpt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0839 time to fit residues: 3.9892 Evaluate side-chains 29 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.023558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.017543 restraints weight = 163844.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.018040 restraints weight = 107070.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.018381 restraints weight = 81812.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.018613 restraints weight = 68085.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.018769 restraints weight = 60369.919| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8759 Z= 0.249 Angle : 0.759 12.584 12627 Z= 0.433 Chirality : 0.046 0.422 1466 Planarity : 0.005 0.068 927 Dihedral : 32.356 172.493 2675 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.34), residues: 569 helix: 1.76 (0.25), residues: 358 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 22 TYR 0.009 0.002 TYR D 100 PHE 0.027 0.003 PHE C 152 HIS 0.009 0.002 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.25 ( 8756) covalent geometry : angle 0.75882 / 0.43 (12618) hydrogen bonds : bond 0.09128 / 6.27 ( 483) hydrogen bonds : angle 3.64550 / 2.54 ( 1221) link_TRANS : bond 0.00389 / 0.19 ( 3) link_TRANS : angle 0.59351 / 0.19 ( 9) *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.9093 (mmp) cc_final: 0.8413 (mmm) REVERT: A 172 MET cc_start: 0.9273 (ppp) cc_final: 0.8939 (ppp) REVERT: A 173 LEU cc_start: 0.9802 (mt) cc_final: 0.9599 (mt) REVERT: D 93 MET cc_start: 0.9545 (mtm) cc_final: 0.9252 (ptm) REVERT: C 153 MET cc_start: 0.9412 (mmt) cc_final: 0.9129 (tpp) REVERT: F 80 MET cc_start: 0.8954 (pmm) cc_final: 0.8635 (pmm) REVERT: F 91 MET cc_start: 0.9065 (mmp) cc_final: 0.8844 (mmm) REVERT: E 151 MET cc_start: 0.9530 (mtt) cc_final: 0.9059 (mmt) REVERT: E 171 ASP cc_start: 0.9534 (m-30) cc_final: 0.9247 (m-30) REVERT: E 172 MET cc_start: 0.9403 (mmt) cc_final: 0.8705 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0852 time to fit residues: 4.0870 Evaluate side-chains 30 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 61 optimal weight: 30.0000 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.017822 restraints weight = 158519.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.018317 restraints weight = 102548.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.018673 restraints weight = 78004.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.018932 restraints weight = 64642.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019080 restraints weight = 56895.703| |-----------------------------------------------------------------------------| r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8759 Z= 0.174 Angle : 0.669 9.593 12627 Z= 0.389 Chirality : 0.044 0.404 1466 Planarity : 0.004 0.039 927 Dihedral : 32.383 172.821 2675 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.34), residues: 569 helix: 2.09 (0.26), residues: 366 sheet: None (None), residues: 0 loop : -1.02 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 111 TYR 0.009 0.001 TYR D 81 PHE 0.013 0.002 PHE C 152 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.17 ( 8756) covalent geometry : angle 0.66895 / 0.39 (12618) hydrogen bonds : bond 0.05943 / 4.13 ( 483) hydrogen bonds : angle 3.32762 / 2.32 ( 1221) link_TRANS : bond 0.00091 / 0.04 ( 3) link_TRANS : angle 0.25382 / 0.13 ( 9) ********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9634 (tmm) cc_final: 0.9383 (ppp) REVERT: B 80 MET cc_start: 0.9093 (mmp) cc_final: 0.8423 (mmm) REVERT: A 151 MET cc_start: 0.9510 (mtt) cc_final: 0.9285 (mtt) REVERT: A 172 MET cc_start: 0.9238 (ppp) cc_final: 0.8892 (ppp) REVERT: A 173 LEU cc_start: 0.9790 (mt) cc_final: 0.9543 (mt) REVERT: D 24 MET cc_start: 0.9374 (ptm) cc_final: 0.9146 (ptm) REVERT: D 93 MET cc_start: 0.9565 (mtm) cc_final: 0.9172 (ptm) REVERT: F 80 MET cc_start: 0.8871 (pmm) cc_final: 0.8465 (pmm) REVERT: F 91 MET cc_start: 0.9057 (mmp) cc_final: 0.8836 (mmm) REVERT: E 171 ASP cc_start: 0.9484 (m-30) cc_final: 0.9236 (m-30) REVERT: E 172 MET cc_start: 0.9440 (mmt) cc_final: 0.8862 (mmm) REVERT: E 210 MET cc_start: 0.8646 (tpt) cc_final: 0.8312 (tpt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0895 time to fit residues: 4.3351 Evaluate side-chains 30 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 40.0000 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.024052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.018130 restraints weight = 157320.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.018576 restraints weight = 99698.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.018928 restraints weight = 74907.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.019188 restraints weight = 61966.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.019347 restraints weight = 54493.998| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8759 Z= 0.153 Angle : 0.628 7.590 12627 Z= 0.370 Chirality : 0.042 0.380 1466 Planarity : 0.003 0.036 927 Dihedral : 32.205 173.996 2675 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.35), residues: 569 helix: 2.44 (0.26), residues: 363 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 22 TYR 0.007 0.001 TYR D 81 PHE 0.014 0.001 PHE C 152 HIS 0.011 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 ( 8756) covalent geometry : angle 0.62838 / 0.37 (12618) hydrogen bonds : bond 0.04757 / 3.29 ( 483) hydrogen bonds : angle 3.11377 / 2.17 ( 1221) link_TRANS : bond 0.00158 / 0.08 ( 3) link_TRANS : angle 0.21775 / 0.12 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.72 seconds wall clock time: 19 minutes 47.20 seconds (1187.20 seconds total)