Starting phenix.real_space_refine on Wed Mar 12 16:37:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lv9_23530/03_2025/7lv9_23530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lv9_23530/03_2025/7lv9_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_2025/7lv9_23530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_2025/7lv9_23530.map" model { file = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_2025/7lv9_23530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lv9_23530/03_2025/7lv9_23530.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 190 5.49 5 S 26 5.16 5 C 4566 2.51 5 N 1515 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 680 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1931 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "H" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1964 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Time building chain proxies: 5.48, per 1000 atoms: 0.67 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: 1.87 Conformation dependent library (CDL) restraints added in 778.4 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 64.7% alpha, 1.7% beta 88 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 3.60 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: 2.98 Time building geometry restraints manager: 2.27 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: 1.160 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8756 Z= 0.194 Angle : 0.639 7.072 12618 Z= 0.385 Chirality : 0.036 0.162 1466 Planarity : 0.004 0.032 927 Dihedral : 27.068 173.114 3714 Min Nonbonded Distance : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.25), residues: 569 helix: -2.29 (0.18), residues: 360 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 57 PHE 0.024 0.002 PHE C 152 TYR 0.024 0.003 TYR D 100 ARG 0.005 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8435 (mtp) cc_final: 0.8220 (ttp) REVERT: E 151 MET cc_start: 0.8408 (mtp) cc_final: 0.7705 (mtt) REVERT: E 176 ILE cc_start: 0.9069 (mt) cc_final: 0.8434 (mt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2574 time to fit residues: 22.6190 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 : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN E 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.022359 restraints weight = 140631.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.022943 restraints weight = 90824.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023391 restraints weight = 67476.860| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8756 Z= 0.317 Angle : 0.670 6.587 12618 Z= 0.398 Chirality : 0.037 0.178 1466 Planarity : 0.006 0.085 927 Dihedral : 30.540 176.745 2675 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.32), residues: 569 helix: 1.44 (0.25), residues: 359 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 131 PHE 0.034 0.003 PHE F 96 TYR 0.014 0.002 TYR D 81 ARG 0.006 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.584 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: 0.9706 (tmm) cc_final: 0.9490 (tmm) REVERT: D 24 MET cc_start: 0.9547 (mtp) cc_final: 0.9261 (ttm) REVERT: C 153 MET cc_start: 0.9274 (mmt) cc_final: 0.8820 (mmm) REVERT: F 91 MET cc_start: 0.9010 (mmp) cc_final: 0.8751 (mmm) REVERT: E 151 MET cc_start: 0.9489 (mtp) cc_final: 0.9246 (mtt) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2210 time to fit residues: 12.9278 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 : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.028403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.021997 restraints weight = 144173.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.022575 restraints weight = 90342.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.023033 restraints weight = 66313.269| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8756 Z= 0.201 Angle : 0.568 6.359 12618 Z= 0.342 Chirality : 0.033 0.178 1466 Planarity : 0.003 0.041 927 Dihedral : 30.609 175.008 2675 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.34), residues: 569 helix: 2.24 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 57 PHE 0.019 0.002 PHE C 152 TYR 0.016 0.002 TYR D 81 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9733 (tmm) cc_final: 0.9522 (tmm) REVERT: B 71 MET cc_start: 0.8858 (tmm) cc_final: 0.8497 (tmm) REVERT: D 24 MET cc_start: 0.9475 (mtp) cc_final: 0.9035 (ttm) REVERT: D 93 MET cc_start: 0.9603 (mtm) cc_final: 0.9228 (ttp) REVERT: F 91 MET cc_start: 0.9025 (mmp) cc_final: 0.8780 (mmm) REVERT: E 151 MET cc_start: 0.9429 (mtp) cc_final: 0.9160 (mtt) REVERT: E 171 ASP cc_start: 0.9452 (m-30) cc_final: 0.9229 (m-30) REVERT: E 172 MET cc_start: 0.9403 (mmt) cc_final: 0.8891 (mmm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2191 time to fit residues: 11.3964 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- 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** C 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.025193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.019217 restraints weight = 162412.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.019680 restraints weight = 107085.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.020010 restraints weight = 81682.631| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8756 Z= 0.313 Angle : 0.666 9.385 12618 Z= 0.393 Chirality : 0.037 0.173 1466 Planarity : 0.006 0.091 927 Dihedral : 31.240 179.866 2675 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 569 helix: 2.21 (0.26), residues: 363 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 131 PHE 0.019 0.002 PHE C 152 TYR 0.017 0.002 TYR D 81 ARG 0.025 0.001 ARG F 76 *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9729 (tmm) cc_final: 0.9315 (ppp) REVERT: B 71 MET cc_start: 0.9231 (tmm) cc_final: 0.8995 (tmm) REVERT: D 24 MET cc_start: 0.9453 (mtp) cc_final: 0.9027 (ttm) REVERT: D 93 MET cc_start: 0.9606 (mtm) cc_final: 0.9224 (ptm) REVERT: C 153 MET cc_start: 0.9399 (mmt) cc_final: 0.8956 (ptt) REVERT: F 91 MET cc_start: 0.9103 (mmp) cc_final: 0.8862 (mmm) REVERT: E 151 MET cc_start: 0.9344 (mtp) cc_final: 0.9031 (mtt) REVERT: E 210 MET cc_start: 0.8837 (tpt) cc_final: 0.8508 (tpt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1991 time to fit residues: 9.5573 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 : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.0670 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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 = 0.2764 r_free = 0.2764 target = 0.025677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.019608 restraints weight = 157294.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.020154 restraints weight = 104296.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.020366 restraints weight = 79268.411| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8756 Z= 0.192 Angle : 0.569 7.388 12618 Z= 0.342 Chirality : 0.034 0.209 1466 Planarity : 0.004 0.049 927 Dihedral : 31.270 177.273 2675 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.22 % Allowed : 1.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.35), residues: 569 helix: 2.59 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 164 PHE 0.013 0.001 PHE C 152 TYR 0.012 0.001 TYR D 81 ARG 0.003 0.000 ARG B 37 *********************** 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 34 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9700 (tmm) cc_final: 0.9484 (tmm) REVERT: B 71 MET cc_start: 0.9245 (tmm) cc_final: 0.9019 (tmm) REVERT: D 24 MET cc_start: 0.9443 (mtp) cc_final: 0.9041 (ttm) REVERT: D 93 MET cc_start: 0.9627 (mtm) cc_final: 0.9111 (ptm) REVERT: C 153 MET cc_start: 0.9388 (mmt) cc_final: 0.8886 (mmp) REVERT: F 91 MET cc_start: 0.9060 (mmp) cc_final: 0.8845 (mmm) REVERT: E 151 MET cc_start: 0.9416 (mtp) cc_final: 0.9149 (mtt) REVERT: E 171 ASP cc_start: 0.9550 (m-30) cc_final: 0.9315 (m-30) REVERT: E 172 MET cc_start: 0.9359 (mmt) cc_final: 0.8786 (mmm) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.2004 time to fit residues: 9.8912 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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 = 0.2695 r_free = 0.2695 target = 0.024049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.018160 restraints weight = 158911.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.018603 restraints weight = 102823.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.018931 restraints weight = 77893.860| |-----------------------------------------------------------------------------| r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8756 Z= 0.264 Angle : 0.637 15.898 12618 Z= 0.375 Chirality : 0.036 0.156 1466 Planarity : 0.004 0.038 927 Dihedral : 31.632 179.665 2675 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.35), residues: 569 helix: 2.28 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.33 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 164 PHE 0.016 0.002 PHE C 152 TYR 0.007 0.001 TYR D 81 ARG 0.004 0.001 ARG A 199 *********************** 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 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9668 (tmm) cc_final: 0.9395 (ppp) REVERT: D 24 MET cc_start: 0.9479 (mtp) cc_final: 0.9008 (ttm) REVERT: D 93 MET cc_start: 0.9606 (mtm) cc_final: 0.9179 (ptm) REVERT: C 153 MET cc_start: 0.9426 (mmt) cc_final: 0.8804 (tpt) REVERT: F 58 MET cc_start: 0.9685 (tmm) cc_final: 0.9423 (tmm) REVERT: E 151 MET cc_start: 0.9350 (mtp) cc_final: 0.9036 (mtt) REVERT: E 172 MET cc_start: 0.9345 (mmt) cc_final: 0.8808 (mmm) REVERT: E 210 MET cc_start: 0.8603 (tpt) cc_final: 0.8247 (tpt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2064 time to fit residues: 9.5629 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.2667 r_free = 0.2667 target = 0.023332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.017649 restraints weight = 161028.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.018073 restraints weight = 101301.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.018388 restraints weight = 75961.341| |-----------------------------------------------------------------------------| r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8756 Z= 0.255 Angle : 0.618 6.158 12618 Z= 0.368 Chirality : 0.035 0.207 1466 Planarity : 0.004 0.058 927 Dihedral : 32.055 178.667 2675 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.34), residues: 569 helix: 2.14 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.14 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 164 PHE 0.013 0.002 PHE C 152 TYR 0.009 0.001 TYR D 100 ARG 0.004 0.001 ARG F 76 *********************** 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 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.9660 (tmm) cc_final: 0.9425 (ppp) REVERT: D 24 MET cc_start: 0.9454 (mtp) cc_final: 0.9109 (ttm) REVERT: D 93 MET cc_start: 0.9626 (mtm) cc_final: 0.9254 (ptm) REVERT: C 153 MET cc_start: 0.9425 (mmt) cc_final: 0.9019 (ptt) REVERT: F 58 MET cc_start: 0.9709 (tmm) cc_final: 0.9436 (tmm) REVERT: F 71 MET cc_start: 0.9569 (ttt) cc_final: 0.9157 (tmm) REVERT: F 91 MET cc_start: 0.9129 (mmp) cc_final: 0.8870 (mmm) REVERT: E 151 MET cc_start: 0.9424 (mtp) cc_final: 0.9165 (mtt) REVERT: E 172 MET cc_start: 0.9363 (mmt) cc_final: 0.8819 (mmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2108 time to fit residues: 10.1136 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.2692 r_free = 0.2692 target = 0.024005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.018044 restraints weight = 157854.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.018567 restraints weight = 99281.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.018937 restraints weight = 74094.864| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8756 Z= 0.180 Angle : 0.574 9.034 12618 Z= 0.342 Chirality : 0.034 0.182 1466 Planarity : 0.003 0.031 927 Dihedral : 31.757 179.025 2675 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.35), residues: 569 helix: 2.53 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 92 PHE 0.012 0.001 PHE C 152 TYR 0.006 0.001 TYR D 100 ARG 0.004 0.000 ARG F 76 *********************** 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 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9476 (mtt) cc_final: 0.9228 (mpp) REVERT: D 24 MET cc_start: 0.9419 (mtp) cc_final: 0.9127 (ttm) REVERT: D 93 MET cc_start: 0.9656 (mtm) cc_final: 0.9325 (mtm) REVERT: C 153 MET cc_start: 0.9415 (mmt) cc_final: 0.9018 (ptt) REVERT: F 58 MET cc_start: 0.9693 (tmm) cc_final: 0.9452 (tmm) REVERT: F 91 MET cc_start: 0.9124 (mmp) cc_final: 0.8896 (mmm) REVERT: E 151 MET cc_start: 0.9470 (mtp) cc_final: 0.9267 (mtt) REVERT: E 172 MET cc_start: 0.9364 (mmt) cc_final: 0.8790 (mmm) REVERT: E 210 MET cc_start: 0.8697 (tpt) cc_final: 0.8359 (tpt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2015 time to fit residues: 9.3678 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 = 0.2613 r_free = 0.2613 target = 0.022573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.017014 restraints weight = 170970.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.017393 restraints weight = 109275.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.017697 restraints weight = 82559.310| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.8220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8756 Z= 0.351 Angle : 0.681 6.406 12618 Z= 0.403 Chirality : 0.039 0.160 1466 Planarity : 0.005 0.039 927 Dihedral : 32.388 177.145 2675 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.34), residues: 569 helix: 1.98 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 164 PHE 0.015 0.002 PHE C 196 TYR 0.009 0.002 TYR C 151 ARG 0.008 0.001 ARG E 133 *********************** 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 29 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.9344 (mtt) cc_final: 0.9090 (mpp) REVERT: D 24 MET cc_start: 0.9421 (mtp) cc_final: 0.8965 (ttm) REVERT: D 93 MET cc_start: 0.9619 (mtm) cc_final: 0.9286 (mtm) REVERT: C 153 MET cc_start: 0.9442 (mmt) cc_final: 0.8818 (tpt) REVERT: F 58 MET cc_start: 0.9624 (tmm) cc_final: 0.9406 (tmm) REVERT: F 91 MET cc_start: 0.9168 (mmp) cc_final: 0.8927 (mmm) REVERT: E 151 MET cc_start: 0.9387 (mtp) cc_final: 0.9060 (mtt) REVERT: E 172 MET cc_start: 0.9409 (mmt) cc_final: 0.8866 (mmm) REVERT: E 210 MET cc_start: 0.8736 (tpt) cc_final: 0.8411 (tpt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2319 time to fit residues: 9.7984 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.022346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.016681 restraints weight = 168556.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.017140 restraints weight = 108700.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.017461 restraints weight = 82456.635| |-----------------------------------------------------------------------------| r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.9087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8756 Z= 0.319 Angle : 0.690 8.854 12618 Z= 0.405 Chirality : 0.038 0.142 1466 Planarity : 0.004 0.032 927 Dihedral : 32.900 175.894 2675 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.34), residues: 569 helix: 1.64 (0.25), residues: 377 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 164 PHE 0.017 0.002 PHE C 152 TYR 0.009 0.002 TYR D 100 ARG 0.006 0.001 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.9261 (mtt) cc_final: 0.9013 (mpp) REVERT: A 210 MET cc_start: 0.9134 (tpt) cc_final: 0.8928 (tpp) REVERT: D 24 MET cc_start: 0.9443 (mtp) cc_final: 0.8975 (ttm) REVERT: D 93 MET cc_start: 0.9656 (mtm) cc_final: 0.9380 (mtm) REVERT: C 153 MET cc_start: 0.9465 (mmt) cc_final: 0.8831 (tpt) REVERT: F 58 MET cc_start: 0.9653 (tmm) cc_final: 0.9425 (tmm) REVERT: E 151 MET cc_start: 0.9455 (mtp) cc_final: 0.9136 (mtt) REVERT: E 172 MET cc_start: 0.9422 (mmt) cc_final: 0.8878 (mmm) REVERT: E 210 MET cc_start: 0.8741 (tpt) cc_final: 0.8416 (tpt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2167 time to fit residues: 8.8274 Evaluate side-chains 24 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.022226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.016564 restraints weight = 171864.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.017011 restraints weight = 110573.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.017333 restraints weight = 84151.699| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.9437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8756 Z= 0.332 Angle : 0.695 7.693 12618 Z= 0.409 Chirality : 0.039 0.196 1466 Planarity : 0.004 0.036 927 Dihedral : 32.970 175.500 2675 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.34), residues: 569 helix: 1.59 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 164 PHE 0.014 0.002 PHE C 152 TYR 0.008 0.002 TYR C 151 ARG 0.006 0.001 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.87 seconds wall clock time: 35 minutes 33.25 seconds (2133.25 seconds total)