Starting phenix.real_space_refine on Fri Aug 22 19:38:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5k_37295/08_2025/8w5k_37295.cif" } resolution = 3.6 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= 0.003 sd= 0.070 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 1 5.49 5 S 22 5.16 5 C 4741 2.51 5 N 1225 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7379 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "F" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.24 Number of scatterers: 7379 At special positions: 0 Unit cell: (94.8024, 104.498, 142.204, 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 22 16.00 P 1 15.00 O 1390 8.00 N 1225 7.00 C 4741 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 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 328.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 37.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 86 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 51 through 58 removed outlier: 4.142A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 44 removed outlier: 4.265A pdb=" N ASN E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 Processing helix chain 'L' and resid 51 through 58 removed outlier: 3.818A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA L 58 " --> pdb=" O MET L 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.604A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 49 through 55 Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 364 through 373 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 62 through 66 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.588A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 361 through 362 removed outlier: 7.437A pdb=" N THR F 361 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN F 89 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 89 " --> pdb=" O PHE F 359 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS F 323 " --> pdb=" O ASP F 319 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 267 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL F 196 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN F 184 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL F 198 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR F 182 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER F 200 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL F 180 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU F 202 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL F 178 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER F 204 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE F 176 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS F 165 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 98 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93 removed outlier: 6.755A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU I 209 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY I 83 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU I 357 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 1926 1.45 - 1.57: 4200 1.57 - 1.69: 2 1.69 - 1.81: 36 Bond restraints: 7538 Sorted by residual: bond pdb=" CG GLU C 19 " pdb=" CD GLU C 19 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.26e+00 bond pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.77e-02 3.19e+03 1.39e+00 bond pdb=" CB PRO E 34 " pdb=" CG PRO E 34 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.39e+00 bond pdb=" CA ASP F 134 " pdb=" CB ASP F 134 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.43e-02 4.89e+03 1.38e+00 bond pdb=" CA VAL K 37 " pdb=" C VAL K 37 " ideal model delta sigma weight residual 1.519 1.532 -0.013 1.14e-02 7.69e+03 1.26e+00 ... (remaining 7533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9954 1.85 - 3.70: 207 3.70 - 5.54: 35 5.54 - 7.39: 14 7.39 - 9.24: 9 Bond angle restraints: 10219 Sorted by residual: angle pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " pdb=" CG GLU C 19 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" C ASN I 133 " pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 125.66 133.77 -8.11 1.85e+00 2.92e-01 1.92e+01 angle pdb=" N GLU C 19 " pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " ideal model delta sigma weight residual 110.28 116.32 -6.04 1.55e+00 4.16e-01 1.52e+01 angle pdb=" CA PRO E 34 " pdb=" N PRO E 34 " pdb=" CD PRO E 34 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.40e+01 angle pdb=" C ASN F 133 " pdb=" N ASP F 134 " pdb=" CA ASP F 134 " ideal model delta sigma weight residual 124.31 130.08 -5.77 1.67e+00 3.59e-01 1.19e+01 ... (remaining 10214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 3998 22.27 - 44.53: 382 44.53 - 66.80: 62 66.80 - 89.06: 12 89.06 - 111.33: 1 Dihedral angle restraints: 4455 sinusoidal: 1737 harmonic: 2718 Sorted by residual: dihedral pdb=" CA ASN F 95 " pdb=" C ASN F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ASN F 133 " pdb=" C ASN F 133 " pdb=" N ASP F 134 " pdb=" CA ASP F 134 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 894 0.047 - 0.095: 207 0.095 - 0.142: 54 0.142 - 0.190: 1 0.190 - 0.237: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CA GLU C 19 " pdb=" N GLU C 19 " pdb=" C GLU C 19 " pdb=" CB GLU C 19 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO E 34 " pdb=" N PRO E 34 " pdb=" C PRO E 34 " pdb=" CB PRO E 34 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CB THR J 129 " pdb=" CA THR J 129 " pdb=" OG1 THR J 129 " pdb=" CG2 THR J 129 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1154 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 33 " -0.056 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO E 34 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 206 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO F 207 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 206 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO I 207 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " -0.022 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 83 2.64 - 3.21: 6562 3.21 - 3.77: 10971 3.77 - 4.34: 14222 4.34 - 4.90: 24985 Nonbonded interactions: 56823 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.095 3.040 nonbonded pdb=" OD1 ASN I 149 " pdb=" NE2 GLN I 169 " model vdw 2.190 3.120 nonbonded pdb=" OG SER I 186 " pdb=" O THR I 194 " model vdw 2.203 3.040 nonbonded pdb=" NE2 GLN I 166 " pdb=" OE2 GLU I 168 " model vdw 2.221 3.120 ... (remaining 56818 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 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = (chain 'I' and resid 49 through 373) } 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: 2.060 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.004 0.059 7538 Z= 0.157 Angle : 0.717 9.239 10219 Z= 0.364 Chirality : 0.043 0.237 1157 Planarity : 0.005 0.082 1298 Dihedral : 17.116 111.328 2695 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.88 % Allowed : 25.82 % Favored : 73.30 % 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 aren not related in a simple way. whole: 0.90 (0.29), residues: 918 helix: 2.28 (0.29), residues: 329 sheet: -0.09 (0.26), residues: 406 loop : -0.69 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 310 TYR 0.020 0.001 TYR I 217 PHE 0.013 0.001 PHE E 50 TRP 0.011 0.001 TRP I 260 HIS 0.002 0.001 HIS I 346 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7538) covalent geometry : angle 0.71722 (10219) hydrogen bonds : bond 0.08966 ( 524) hydrogen bonds : angle 5.70391 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7942 (ptpt) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.0892 time to fit residues: 13.9495 Evaluate side-chains 103 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain L residue 56 MET Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN I 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.186680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169941 restraints weight = 7952.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168327 restraints weight = 17843.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168498 restraints weight = 18215.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167713 restraints weight = 12846.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167896 restraints weight = 11578.985| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7538 Z= 0.170 Angle : 0.681 8.088 10219 Z= 0.341 Chirality : 0.044 0.164 1157 Planarity : 0.004 0.055 1298 Dihedral : 8.025 110.522 1033 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.04 % Allowed : 23.43 % Favored : 71.54 % 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 aren not related in a simple way. whole: 0.87 (0.29), residues: 918 helix: 2.39 (0.29), residues: 329 sheet: -0.15 (0.26), residues: 410 loop : -0.86 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 261 TYR 0.016 0.001 TYR I 217 PHE 0.012 0.001 PHE I 340 TRP 0.013 0.001 TRP I 260 HIS 0.006 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7538) covalent geometry : angle 0.68069 (10219) hydrogen bonds : bond 0.03191 ( 524) hydrogen bonds : angle 5.00169 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 139 average time/residue: 0.0823 time to fit residues: 15.4832 Evaluate side-chains 122 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN F 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168516 restraints weight = 7973.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166379 restraints weight = 17449.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158533 restraints weight = 17682.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155954 restraints weight = 11664.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155380 restraints weight = 13555.009| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7538 Z= 0.139 Angle : 0.642 7.254 10219 Z= 0.319 Chirality : 0.042 0.160 1157 Planarity : 0.004 0.053 1298 Dihedral : 7.317 106.792 1025 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.67 % Allowed : 24.06 % Favored : 70.28 % 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 aren not related in a simple way. whole: 0.92 (0.29), residues: 918 helix: 2.34 (0.29), residues: 331 sheet: -0.13 (0.26), residues: 410 loop : -0.68 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 47 TYR 0.010 0.001 TYR I 307 PHE 0.010 0.001 PHE I 340 TRP 0.011 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7538) covalent geometry : angle 0.64230 (10219) hydrogen bonds : bond 0.02898 ( 524) hydrogen bonds : angle 4.84119 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.5051 (pt) REVERT: M 26 ASN cc_start: 0.7714 (t0) cc_final: 0.7132 (p0) outliers start: 45 outliers final: 31 residues processed: 132 average time/residue: 0.0748 time to fit residues: 13.2850 Evaluate side-chains 126 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.185125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168878 restraints weight = 8063.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167112 restraints weight = 17056.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166845 restraints weight = 16763.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165042 restraints weight = 14656.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165165 restraints weight = 15335.021| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7538 Z= 0.140 Angle : 0.626 7.840 10219 Z= 0.311 Chirality : 0.042 0.161 1157 Planarity : 0.004 0.051 1298 Dihedral : 7.083 102.586 1025 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.79 % Allowed : 24.94 % Favored : 69.27 % 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 aren not related in a simple way. whole: 0.96 (0.29), residues: 918 helix: 2.36 (0.29), residues: 333 sheet: -0.11 (0.26), residues: 410 loop : -0.63 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 47 TYR 0.015 0.001 TYR I 217 PHE 0.010 0.001 PHE I 340 TRP 0.011 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7538) covalent geometry : angle 0.62620 (10219) hydrogen bonds : bond 0.02793 ( 524) hydrogen bonds : angle 4.72958 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5126 (pt) REVERT: I 158 SER cc_start: 0.6747 (OUTLIER) cc_final: 0.6415 (p) outliers start: 46 outliers final: 37 residues processed: 132 average time/residue: 0.0823 time to fit residues: 14.7829 Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.184635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167115 restraints weight = 7940.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165216 restraints weight = 18846.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.165676 restraints weight = 17064.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165139 restraints weight = 12369.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165213 restraints weight = 11847.478| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7538 Z= 0.139 Angle : 0.630 7.914 10219 Z= 0.313 Chirality : 0.042 0.163 1157 Planarity : 0.004 0.050 1298 Dihedral : 6.951 98.218 1025 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 7.18 % Allowed : 24.56 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.29), residues: 918 helix: 2.44 (0.29), residues: 321 sheet: -0.09 (0.26), residues: 410 loop : -0.18 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 47 TYR 0.008 0.001 TYR I 307 PHE 0.016 0.001 PHE L 42 TRP 0.011 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7538) covalent geometry : angle 0.63038 (10219) hydrogen bonds : bond 0.02768 ( 524) hydrogen bonds : angle 4.65714 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8340 (tp) REVERT: L 61 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5128 (pt) REVERT: M 38 TYR cc_start: 0.6687 (t80) cc_final: 0.6463 (t80) outliers start: 57 outliers final: 42 residues processed: 138 average time/residue: 0.0785 time to fit residues: 14.8440 Evaluate side-chains 135 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.4930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.186594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170028 restraints weight = 7911.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168388 restraints weight = 18487.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.168153 restraints weight = 17924.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166918 restraints weight = 13420.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167204 restraints weight = 11606.085| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7538 Z= 0.126 Angle : 0.608 7.602 10219 Z= 0.302 Chirality : 0.041 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.646 90.054 1025 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.30 % Allowed : 25.19 % Favored : 68.51 % 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 aren not related in a simple way. whole: 1.15 (0.29), residues: 918 helix: 2.48 (0.29), residues: 321 sheet: -0.05 (0.26), residues: 410 loop : -0.15 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 85 TYR 0.012 0.001 TYR I 217 PHE 0.013 0.001 PHE F 120 TRP 0.011 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7538) covalent geometry : angle 0.60774 (10219) hydrogen bonds : bond 0.02645 ( 524) hydrogen bonds : angle 4.56510 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 40 MET cc_start: 0.5435 (mmt) cc_final: 0.5081 (mpp) REVERT: J 113 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8521 (tp) REVERT: F 275 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7111 (pp) REVERT: I 94 MET cc_start: 0.7694 (tpp) cc_final: 0.7397 (tpt) outliers start: 50 outliers final: 37 residues processed: 135 average time/residue: 0.0815 time to fit residues: 14.6994 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 17 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 121 GLN I 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.182511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165889 restraints weight = 8089.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.164239 restraints weight = 18617.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.164004 restraints weight = 17278.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162309 restraints weight = 14309.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162257 restraints weight = 15166.907| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7538 Z= 0.171 Angle : 0.666 9.993 10219 Z= 0.328 Chirality : 0.043 0.162 1157 Planarity : 0.004 0.050 1298 Dihedral : 6.629 87.240 1025 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.30 % Allowed : 25.69 % Favored : 68.01 % 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 aren not related in a simple way. whole: 0.99 (0.29), residues: 918 helix: 2.36 (0.29), residues: 333 sheet: -0.11 (0.26), residues: 410 loop : -0.55 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 310 TYR 0.008 0.001 TYR I 307 PHE 0.015 0.001 PHE F 120 TRP 0.013 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7538) covalent geometry : angle 0.66644 (10219) hydrogen bonds : bond 0.02861 ( 524) hydrogen bonds : angle 4.64844 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.219 Fit side-chains REVERT: J 113 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8705 (tp) REVERT: L 54 MET cc_start: 0.8423 (tmm) cc_final: 0.7970 (tpp) REVERT: F 275 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7099 (pp) REVERT: I 94 MET cc_start: 0.7740 (tpp) cc_final: 0.7469 (tpt) outliers start: 50 outliers final: 42 residues processed: 132 average time/residue: 0.0730 time to fit residues: 13.2053 Evaluate side-chains 135 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 17 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 303 ILE Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.180868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163812 restraints weight = 8113.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162429 restraints weight = 17279.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162271 restraints weight = 16659.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160906 restraints weight = 14455.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160996 restraints weight = 14865.705| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7538 Z= 0.207 Angle : 0.722 11.422 10219 Z= 0.357 Chirality : 0.044 0.216 1157 Planarity : 0.004 0.051 1298 Dihedral : 6.766 87.988 1025 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.68 % Allowed : 25.44 % Favored : 67.88 % 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 aren not related in a simple way. whole: 0.80 (0.29), residues: 918 helix: 2.22 (0.28), residues: 333 sheet: -0.22 (0.26), residues: 410 loop : -0.65 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 315 TYR 0.008 0.001 TYR F 232 PHE 0.019 0.002 PHE F 120 TRP 0.015 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7538) covalent geometry : angle 0.72177 (10219) hydrogen bonds : bond 0.03159 ( 524) hydrogen bonds : angle 4.77540 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 0.198 Fit side-chains REVERT: K 36 TRP cc_start: 0.6695 (t60) cc_final: 0.6494 (t60) REVERT: L 54 MET cc_start: 0.8488 (tmm) cc_final: 0.8106 (tpp) REVERT: F 275 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7135 (pp) REVERT: I 94 MET cc_start: 0.7760 (tpp) cc_final: 0.7483 (tpt) outliers start: 53 outliers final: 45 residues processed: 130 average time/residue: 0.0670 time to fit residues: 11.9633 Evaluate side-chains 132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 86 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 17 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 303 ILE Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 156 GLN I 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.166540 restraints weight = 7978.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156927 restraints weight = 15827.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152351 restraints weight = 14049.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153012 restraints weight = 15236.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154060 restraints weight = 11179.424| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7538 Z= 0.164 Angle : 0.694 11.194 10219 Z= 0.341 Chirality : 0.043 0.168 1157 Planarity : 0.004 0.050 1298 Dihedral : 6.481 83.832 1023 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.30 % Allowed : 26.45 % Favored : 67.25 % 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 aren not related in a simple way. whole: 0.82 (0.29), residues: 918 helix: 2.23 (0.29), residues: 333 sheet: -0.22 (0.26), residues: 410 loop : -0.55 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 310 TYR 0.009 0.001 TYR I 307 PHE 0.017 0.001 PHE F 120 TRP 0.013 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7538) covalent geometry : angle 0.69423 (10219) hydrogen bonds : bond 0.02918 ( 524) hydrogen bonds : angle 4.70027 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 89 time to evaluate : 0.182 Fit side-chains REVERT: K 36 TRP cc_start: 0.6841 (t60) cc_final: 0.6515 (t60) REVERT: L 54 MET cc_start: 0.8508 (tmm) cc_final: 0.8040 (tpp) REVERT: F 275 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7099 (pp) REVERT: I 94 MET cc_start: 0.7889 (tpp) cc_final: 0.7633 (tpt) outliers start: 50 outliers final: 43 residues processed: 127 average time/residue: 0.0653 time to fit residues: 11.6744 Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.183424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166857 restraints weight = 7983.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165335 restraints weight = 17644.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165110 restraints weight = 17368.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163996 restraints weight = 13275.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163998 restraints weight = 12347.091| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7538 Z= 0.133 Angle : 0.677 11.313 10219 Z= 0.332 Chirality : 0.042 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.227 78.673 1023 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.29 % Allowed : 27.20 % Favored : 67.51 % 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 aren not related in a simple way. whole: 0.89 (0.29), residues: 918 helix: 2.24 (0.29), residues: 333 sheet: -0.17 (0.26), residues: 410 loop : -0.47 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 310 TYR 0.015 0.001 TYR I 217 PHE 0.016 0.001 PHE F 120 TRP 0.012 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7538) covalent geometry : angle 0.67709 (10219) hydrogen bonds : bond 0.02722 ( 524) hydrogen bonds : angle 4.59189 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.275 Fit side-chains REVERT: K 36 TRP cc_start: 0.6653 (t60) cc_final: 0.6323 (t60) REVERT: L 54 MET cc_start: 0.8444 (tmm) cc_final: 0.7980 (tpp) REVERT: F 275 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7088 (pp) REVERT: I 94 MET cc_start: 0.7725 (tpp) cc_final: 0.7446 (tpt) outliers start: 42 outliers final: 37 residues processed: 121 average time/residue: 0.0731 time to fit residues: 12.3715 Evaluate side-chains 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 303 ILE Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164702 restraints weight = 8017.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163475 restraints weight = 18402.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.163641 restraints weight = 16243.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163360 restraints weight = 12693.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163279 restraints weight = 12424.178| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7538 Z= 0.159 Angle : 0.695 11.677 10219 Z= 0.341 Chirality : 0.043 0.162 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.304 80.012 1023 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.29 % Allowed : 27.20 % Favored : 67.51 % 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 aren not related in a simple way. whole: 0.88 (0.29), residues: 918 helix: 2.22 (0.29), residues: 333 sheet: -0.16 (0.26), residues: 410 loop : -0.51 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 310 TYR 0.008 0.001 TYR I 307 PHE 0.018 0.001 PHE F 120 TRP 0.013 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7538) covalent geometry : angle 0.69549 (10219) hydrogen bonds : bond 0.02855 ( 524) hydrogen bonds : angle 4.59513 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.61 seconds wall clock time: 20 minutes 57.48 seconds (1257.48 seconds total)