Starting phenix.real_space_refine on Tue Mar 3 18:44:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lv9_23530/03_2026/7lv9_23530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lv9_23530/03_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_23530/03_2026/7lv9_23530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_2026/7lv9_23530.map" model { file = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_2026/7lv9_23530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_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-5986/lib/python3.9/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: 1.94, per 1000 atoms: 0.24 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: 0.91 Conformation dependent library (CDL) restraints added in 199.1 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: 1.22 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: 1.58 Time building geometry restraints manager: 1.14 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: 0.00 - 1.41: 12062 1.41 - 2.83: 505 2.83 - 4.24: 36 4.24 - 5.66: 10 5.66 - 7.07: 5 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: 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 - 0.032: 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: 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: 1.510 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- 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 8759 Z= 0.168 Angle : 0.639 7.072 12627 Z= 0.385 Chirality : 0.036 0.162 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 covalent geometry : bond 0.00349 ( 8756) covalent geometry : angle 0.63931 (12618) hydrogen bonds : bond 0.20477 ( 483) hydrogen bonds : angle 5.61629 ( 1221) link_TRANS : bond 0.00674 ( 3) link_TRANS : angle 0.80364 ( 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 : 0.142 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: 0.1051 time to fit residues: 9.2507 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 : 0.213 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.021069 restraints weight = 152405.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.021536 restraints weight = 101718.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.021844 restraints weight = 77641.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.022129 restraints weight = 65434.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.022304 restraints weight = 57709.046| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 8759 Z= 0.323 Angle : 0.739 6.419 12627 Z= 0.433 Chirality : 0.040 0.173 1466 Planarity : 0.007 0.118 927 Dihedral : 30.784 178.441 2675 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.22 % Allowed : 3.90 % Favored : 95.88 % 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: 0.33 (0.32), residues: 569 helix: 1.22 (0.25), residues: 359 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 18 TYR 0.015 0.002 TYR D 81 PHE 0.039 0.004 PHE F 96 HIS 0.008 0.002 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 8756) covalent geometry : angle 0.73930 (12618) hydrogen bonds : bond 0.08505 ( 483) hydrogen bonds : angle 3.43160 ( 1221) link_TRANS : bond 0.00250 ( 3) link_TRANS : angle 0.49787 ( 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 43 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.191 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: 0.9731 (tmm) cc_final: 0.9505 (tmm) REVERT: B 80 MET cc_start: 0.8284 (mtp) cc_final: 0.8083 (mpp) REVERT: D 24 MET cc_start: 0.9525 (mtp) cc_final: 0.9188 (ttm) REVERT: D 93 MET cc_start: 0.9619 (mtm) cc_final: 0.9190 (ttp) REVERT: C 153 MET cc_start: 0.9308 (mmt) cc_final: 0.8864 (mmm) REVERT: F 91 MET cc_start: 0.9066 (mmp) cc_final: 0.8805 (mmm) REVERT: E 151 MET cc_start: 0.9415 (mtp) cc_final: 0.9178 (mtt) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0971 time to fit residues: 5.7861 Evaluate side-chains 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** D 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.024153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.018345 restraints weight = 165596.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.018817 restraints weight = 111941.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.019148 restraints weight = 86546.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.019328 restraints weight = 72662.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.019506 restraints weight = 65158.499| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 8759 Z= 0.313 Angle : 0.728 5.737 12627 Z= 0.432 Chirality : 0.039 0.186 1466 Planarity : 0.006 0.102 927 Dihedral : 31.828 179.749 2675 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % 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 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: 0.74 (0.33), residues: 569 helix: 1.61 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 76 TYR 0.024 0.002 TYR D 81 PHE 0.023 0.003 PHE C 196 HIS 0.006 0.002 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 8756) covalent geometry : angle 0.72773 (12618) hydrogen bonds : bond 0.07142 ( 483) hydrogen bonds : angle 3.67819 ( 1221) link_TRANS : bond 0.00396 ( 3) link_TRANS : angle 0.52728 ( 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 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9780 (tmm) cc_final: 0.9458 (ppp) REVERT: B 71 MET cc_start: 0.9289 (tmm) cc_final: 0.8792 (tmm) REVERT: D 24 MET cc_start: 0.9358 (mtp) cc_final: 0.9061 (ttm) REVERT: D 93 MET cc_start: 0.9618 (mtm) cc_final: 0.9224 (ptm) REVERT: C 153 MET cc_start: 0.9448 (mmt) cc_final: 0.9003 (ptt) REVERT: F 91 MET cc_start: 0.9088 (mmp) cc_final: 0.8881 (mmm) REVERT: E 151 MET cc_start: 0.9269 (mtp) cc_final: 0.9067 (mtt) REVERT: E 172 MET cc_start: 0.9454 (mmt) cc_final: 0.8959 (mmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0827 time to fit residues: 3.9896 Evaluate side-chains 26 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.017383 restraints weight = 166053.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.017790 restraints weight = 106069.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.018102 restraints weight = 80633.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.018223 restraints weight = 67654.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.018445 restraints weight = 61815.628| |-----------------------------------------------------------------------------| r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8759 Z= 0.308 Angle : 0.687 6.095 12627 Z= 0.410 Chirality : 0.038 0.161 1466 Planarity : 0.005 0.044 927 Dihedral : 32.253 175.996 2675 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 0.92 (0.34), residues: 569 helix: 1.70 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 76 TYR 0.014 0.002 TYR D 81 PHE 0.018 0.002 PHE C 152 HIS 0.005 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 8756) covalent geometry : angle 0.68692 (12618) hydrogen bonds : bond 0.08163 ( 483) hydrogen bonds : angle 3.72260 ( 1221) link_TRANS : bond 0.00370 ( 3) link_TRANS : angle 0.66312 ( 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 : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9760 (tmm) cc_final: 0.9499 (ppp) REVERT: B 71 MET cc_start: 0.9333 (tmm) cc_final: 0.9087 (tmm) REVERT: A 173 LEU cc_start: 0.9766 (mt) cc_final: 0.9545 (mt) REVERT: D 24 MET cc_start: 0.9483 (mtp) cc_final: 0.9053 (ttm) REVERT: D 93 MET cc_start: 0.9563 (mtm) cc_final: 0.9210 (ptm) REVERT: C 153 MET cc_start: 0.9421 (mmt) cc_final: 0.9016 (ptt) REVERT: F 58 MET cc_start: 0.9688 (tmm) cc_final: 0.9459 (tmm) REVERT: F 71 MET cc_start: 0.9627 (ttt) cc_final: 0.8947 (tmm) REVERT: F 91 MET cc_start: 0.9096 (mmp) cc_final: 0.8879 (mmm) REVERT: E 151 MET cc_start: 0.9336 (mtp) cc_final: 0.9011 (mtt) REVERT: E 172 MET cc_start: 0.9403 (mmt) cc_final: 0.8811 (mmm) REVERT: E 210 MET cc_start: 0.8952 (tpt) cc_final: 0.8595 (tpt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0912 time to fit residues: 4.3551 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 : 0.212 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 0.0170 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 overall best weight: 3.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.023334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.017596 restraints weight = 163638.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.018040 restraints weight = 102394.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.018368 restraints weight = 76702.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.018608 restraints weight = 63724.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.018732 restraints weight = 56081.631| |-----------------------------------------------------------------------------| r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8759 Z= 0.205 Angle : 0.612 7.823 12627 Z= 0.366 Chirality : 0.035 0.218 1466 Planarity : 0.003 0.036 927 Dihedral : 32.275 178.848 2675 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.43 % Allowed : 1.08 % 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: 1.48 (0.34), residues: 569 helix: 2.11 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -1.19 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 126 TYR 0.007 0.001 TYR D 81 PHE 0.011 0.001 PHE C 152 HIS 0.005 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8756) covalent geometry : angle 0.61207 (12618) hydrogen bonds : bond 0.05274 ( 483) hydrogen bonds : angle 3.27408 ( 1221) link_TRANS : bond 0.00220 ( 3) link_TRANS : angle 0.62911 ( 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 35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 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: 0.9744 (tmm) cc_final: 0.9496 (ppp) REVERT: A 173 LEU cc_start: 0.9747 (mt) cc_final: 0.9534 (mt) REVERT: D 24 MET cc_start: 0.9412 (mtp) cc_final: 0.8991 (ttm) REVERT: D 93 MET cc_start: 0.9591 (mtm) cc_final: 0.9212 (ptm) REVERT: C 153 MET cc_start: 0.9406 (mmt) cc_final: 0.8963 (mmp) REVERT: F 58 MET cc_start: 0.9692 (tmm) cc_final: 0.9401 (tmm) REVERT: F 71 MET cc_start: 0.9598 (ttt) cc_final: 0.9160 (tmm) REVERT: F 91 MET cc_start: 0.9120 (mmp) cc_final: 0.8859 (mmm) REVERT: E 151 MET cc_start: 0.9349 (mtp) cc_final: 0.9038 (mtt) REVERT: E 172 MET cc_start: 0.9404 (mmt) cc_final: 0.8862 (mmm) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0862 time to fit residues: 4.4631 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 : 0.206 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.016832 restraints weight = 167842.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.017328 restraints weight = 109529.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.017659 restraints weight = 82749.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.017865 restraints weight = 68908.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.018008 restraints weight = 61034.584| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8759 Z= 0.296 Angle : 0.687 6.058 12627 Z= 0.407 Chirality : 0.038 0.152 1466 Planarity : 0.005 0.038 927 Dihedral : 32.658 175.352 2675 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.34), residues: 569 helix: 1.68 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.009 0.001 TYR C 151 PHE 0.014 0.002 PHE C 152 HIS 0.006 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 8756) covalent geometry : angle 0.68629 (12618) hydrogen bonds : bond 0.08373 ( 483) hydrogen bonds : angle 3.58442 ( 1221) link_TRANS : bond 0.00348 ( 3) link_TRANS : angle 0.98332 ( 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 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9722 (tmm) cc_final: 0.9521 (tmm) REVERT: A 173 LEU cc_start: 0.9796 (mt) cc_final: 0.9595 (mt) REVERT: D 24 MET cc_start: 0.9449 (mtp) cc_final: 0.8972 (ttm) REVERT: D 93 MET cc_start: 0.9604 (mtm) cc_final: 0.9293 (ptm) REVERT: C 153 MET cc_start: 0.9438 (mmt) cc_final: 0.8801 (tpt) REVERT: F 58 MET cc_start: 0.9636 (tmm) cc_final: 0.9397 (tmm) REVERT: F 91 MET cc_start: 0.9196 (mmp) cc_final: 0.8941 (mmm) REVERT: E 172 MET cc_start: 0.9428 (mmt) cc_final: 0.8894 (mmm) REVERT: E 210 MET cc_start: 0.8612 (tpt) cc_final: 0.8281 (tpt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0890 time to fit residues: 4.0499 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 : 0.213 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.022676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.016987 restraints weight = 165606.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.017453 restraints weight = 106594.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.017790 restraints weight = 80849.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.017912 restraints weight = 67000.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.018134 restraints weight = 61183.352| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8759 Z= 0.227 Angle : 0.628 6.068 12627 Z= 0.373 Chirality : 0.036 0.161 1466 Planarity : 0.004 0.030 927 Dihedral : 32.732 176.485 2675 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: 1.48 (0.35), residues: 569 helix: 2.03 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 53 TYR 0.006 0.001 TYR C 151 PHE 0.012 0.002 PHE C 152 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8756) covalent geometry : angle 0.62760 (12618) hydrogen bonds : bond 0.06125 ( 483) hydrogen bonds : angle 3.35719 ( 1221) link_TRANS : bond 0.00222 ( 3) link_TRANS : angle 0.55147 ( 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 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9707 (tmm) cc_final: 0.9484 (ppp) REVERT: A 173 LEU cc_start: 0.9791 (mt) cc_final: 0.9574 (mt) REVERT: D 24 MET cc_start: 0.9421 (mtp) cc_final: 0.8966 (ttm) REVERT: D 93 MET cc_start: 0.9619 (mtm) cc_final: 0.9267 (ptm) REVERT: C 153 MET cc_start: 0.9407 (mmt) cc_final: 0.8784 (tpt) REVERT: F 58 MET cc_start: 0.9623 (tmm) cc_final: 0.9394 (tmm) REVERT: F 91 MET cc_start: 0.9269 (mmp) cc_final: 0.9010 (mmm) REVERT: E 136 MET cc_start: 0.9598 (ttm) cc_final: 0.9291 (ptp) REVERT: E 172 MET cc_start: 0.9421 (mmt) cc_final: 0.8876 (mmm) REVERT: E 210 MET cc_start: 0.8655 (tpt) cc_final: 0.8314 (tpt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0917 time to fit residues: 4.1120 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 : 0.177 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2599 r_free = 0.2599 target = 0.022224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.016633 restraints weight = 171872.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.017088 restraints weight = 109067.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.017417 restraints weight = 82984.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.017632 restraints weight = 68942.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.017748 restraints weight = 60964.975| |-----------------------------------------------------------------------------| r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.8529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8759 Z= 0.280 Angle : 0.663 5.664 12627 Z= 0.394 Chirality : 0.037 0.153 1466 Planarity : 0.004 0.032 927 Dihedral : 32.803 176.032 2675 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 1.20 (0.34), residues: 569 helix: 1.72 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 199 TYR 0.008 0.001 TYR C 151 PHE 0.013 0.002 PHE C 152 HIS 0.006 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 8756) covalent geometry : angle 0.66270 (12618) hydrogen bonds : bond 0.08294 ( 483) hydrogen bonds : angle 3.46437 ( 1221) link_TRANS : bond 0.00325 ( 3) link_TRANS : angle 0.63533 ( 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 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.9787 (mt) cc_final: 0.9577 (mt) REVERT: A 210 MET cc_start: 0.9076 (tpt) cc_final: 0.8872 (tpp) REVERT: D 24 MET cc_start: 0.9419 (mtp) cc_final: 0.8936 (ttm) REVERT: D 93 MET cc_start: 0.9618 (mtm) cc_final: 0.9259 (mtm) REVERT: C 153 MET cc_start: 0.9405 (mmt) cc_final: 0.8787 (tpt) REVERT: F 58 MET cc_start: 0.9591 (tmm) cc_final: 0.9360 (tmm) REVERT: E 136 MET cc_start: 0.9610 (ttm) cc_final: 0.9361 (ptm) REVERT: E 172 MET cc_start: 0.9424 (mmt) cc_final: 0.8872 (mmm) REVERT: E 210 MET cc_start: 0.8672 (tpt) cc_final: 0.8338 (tpt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0879 time to fit residues: 3.9922 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 : 0.133 ------------------------------------------------------------------------------- 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: 10.0000 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 0.2980 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2622 r_free = 0.2622 target = 0.022411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.016687 restraints weight = 168604.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.017189 restraints weight = 107868.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.017513 restraints weight = 81001.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.017745 restraints weight = 67347.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.017895 restraints weight = 59330.021| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8759 Z= 0.251 Angle : 0.646 5.720 12627 Z= 0.385 Chirality : 0.037 0.149 1466 Planarity : 0.004 0.036 927 Dihedral : 32.927 175.854 2675 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 1.26 (0.35), residues: 569 helix: 1.78 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.04 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 199 TYR 0.008 0.001 TYR C 151 PHE 0.011 0.002 PHE C 152 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 8756) covalent geometry : angle 0.64560 (12618) hydrogen bonds : bond 0.06552 ( 483) hydrogen bonds : angle 3.41294 ( 1221) link_TRANS : bond 0.00251 ( 3) link_TRANS : angle 0.56298 ( 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 30 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9707 (tmm) cc_final: 0.9472 (ppp) REVERT: A 173 LEU cc_start: 0.9801 (mt) cc_final: 0.9597 (mt) REVERT: A 210 MET cc_start: 0.9127 (tpt) cc_final: 0.8905 (tpp) REVERT: D 24 MET cc_start: 0.9406 (mtp) cc_final: 0.8958 (ttm) REVERT: D 93 MET cc_start: 0.9644 (mtm) cc_final: 0.9304 (mtm) REVERT: C 153 MET cc_start: 0.9436 (mmt) cc_final: 0.8808 (tpt) REVERT: F 58 MET cc_start: 0.9623 (tmm) cc_final: 0.9378 (tmm) REVERT: E 136 MET cc_start: 0.9598 (ttm) cc_final: 0.9368 (ptm) REVERT: E 172 MET cc_start: 0.9432 (mmt) cc_final: 0.8887 (mmm) REVERT: E 210 MET cc_start: 0.8692 (tpt) cc_final: 0.8352 (tpt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0912 time to fit residues: 3.9704 Evaluate side-chains 25 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.023219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.017606 restraints weight = 157648.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.018146 restraints weight = 95482.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.018535 restraints weight = 69359.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.018804 restraints weight = 56236.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.018916 restraints weight = 48194.445| |-----------------------------------------------------------------------------| r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8759 Z= 0.170 Angle : 0.602 9.051 12627 Z= 0.356 Chirality : 0.036 0.228 1466 Planarity : 0.003 0.031 927 Dihedral : 32.557 176.085 2675 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 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 (0.36), residues: 569 helix: 2.13 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.00 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 76 TYR 0.005 0.001 TYR D 81 PHE 0.009 0.001 PHE D 48 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8756) covalent geometry : angle 0.60236 (12618) hydrogen bonds : bond 0.04262 ( 483) hydrogen bonds : angle 3.06824 ( 1221) link_TRANS : bond 0.00133 ( 3) link_TRANS : angle 0.33233 ( 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 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.9486 (mtp) cc_final: 0.9117 (ttm) REVERT: D 93 MET cc_start: 0.9584 (mtm) cc_final: 0.9340 (mtm) REVERT: C 153 MET cc_start: 0.9541 (mmt) cc_final: 0.9223 (mmp) REVERT: F 58 MET cc_start: 0.9734 (tmm) cc_final: 0.9520 (tmm) REVERT: F 91 MET cc_start: 0.9342 (mmp) cc_final: 0.9085 (mmm) REVERT: E 171 ASP cc_start: 0.9616 (m-30) cc_final: 0.8987 (t70) REVERT: E 172 MET cc_start: 0.9503 (mmt) cc_final: 0.8806 (mmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0780 time to fit residues: 3.6484 Evaluate side-chains 26 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.022402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.016877 restraints weight = 166665.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.017364 restraints weight = 103897.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.017712 restraints weight = 77577.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.017895 restraints weight = 63498.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.018077 restraints weight = 56575.630| |-----------------------------------------------------------------------------| r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8759 Z= 0.216 Angle : 0.642 16.103 12627 Z= 0.372 Chirality : 0.036 0.226 1466 Planarity : 0.004 0.031 927 Dihedral : 32.524 176.485 2675 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 1.61 (0.35), residues: 569 helix: 2.08 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.07 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 114 TYR 0.006 0.001 TYR C 151 PHE 0.011 0.002 PHE C 152 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8756) covalent geometry : angle 0.64212 (12618) hydrogen bonds : bond 0.05902 ( 483) hydrogen bonds : angle 3.22836 ( 1221) link_TRANS : bond 0.00196 ( 3) link_TRANS : angle 0.48225 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1145.86 seconds wall clock time: 20 minutes 35.10 seconds (1235.10 seconds total)