Starting phenix.real_space_refine on Thu Jul 2 15:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2026/8csz_26976.map" } resolution = 3.2 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= -0.001 sd= 0.028 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 236 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 4741 2.51 5 N 1654 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3950 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 67} Link IDs: {'rna2p': 25, 'rna3p': 158} Chain breaks: 2 Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 661 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "E" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2125 SG CYS D 265 82.445 57.202 49.318 1.00 89.87 S Time building chain proxies: 1.60, per 1000 atoms: 0.18 Number of scatterers: 8948 At special positions: 0 Unit cell: (99.51, 111.28, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 236 15.00 Mg 2 11.99 O 2287 8.00 N 1654 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: 0.78 Conformation dependent library (CDL) restraints added in 118.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 265 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 268 " 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 34.8% alpha, 17.8% beta 82 base pairs and 139 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.413A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.723A pdb=" N ILE D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 265 through 275 Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.715A pdb=" N GLU D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.870A pdb=" N VAL D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.692A pdb=" N TYR D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 423 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 17 removed outlier: 5.180A pdb=" N MET D 15 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 6 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 3.988A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 79 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.593A pdb=" N GLN D 432 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 392 through 395 removed outlier: 5.883A pdb=" N LEU D 393 " --> pdb=" O MET D 389 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET D 389 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 395 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 386 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.997A pdb=" N GLY D 460 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 469 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER D 458 " --> pdb=" O PHE D 469 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 471 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER D 456 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 444 " --> pdb=" O LEU D 485 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 139 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 0.97 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: 1542 1.33 - 1.45: 3518 1.45 - 1.57: 4051 1.57 - 1.69: 467 1.69 - 1.80: 42 Bond restraints: 9620 Sorted by residual: bond pdb=" C3' DT E 117 " pdb=" C2' DT E 117 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.81e+00 bond pdb=" O4' DT E 117 " pdb=" C1' DT E 117 " ideal model delta sigma weight residual 1.420 1.391 0.029 1.10e-02 8.26e+03 7.19e+00 bond pdb=" C3' DG E 119 " pdb=" O3' DG E 119 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.17e+00 bond pdb=" C3' DT B 30 " pdb=" O3' DT B 30 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" C3' DT B 32 " pdb=" C2' DT B 32 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.37e+00 ... (remaining 9615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13431 1.54 - 3.08: 594 3.08 - 4.62: 61 4.62 - 6.16: 12 6.16 - 7.70: 4 Bond angle restraints: 14102 Sorted by residual: angle pdb=" O4' DC B 25 " pdb=" C4' DC B 25 " pdb=" C3' DC B 25 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT B 30 " pdb=" C4 DT B 30 " pdb=" O4 DT B 30 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT B 32 " pdb=" C4 DT B 32 " pdb=" O4 DT B 32 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT B 23 " pdb=" C4 DT B 23 " pdb=" O4 DT B 23 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT B 33 " pdb=" C4 DT B 33 " pdb=" O4 DT B 33 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 14097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 4870 34.92 - 69.84: 331 69.84 - 104.77: 15 104.77 - 139.69: 6 139.69 - 174.61: 8 Dihedral angle restraints: 5230 sinusoidal: 3795 harmonic: 1435 Sorted by residual: dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 40.92 159.08 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C C 94 " pdb=" C1' C C 94 " pdb=" N1 C C 94 " pdb=" C2 C C 94 " ideal model delta sinusoidal sigma weight residual 232.00 57.39 174.61 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U C 107 " pdb=" C1' U C 107 " pdb=" N1 U C 107 " pdb=" C2 U C 107 " ideal model delta sinusoidal sigma weight residual -128.00 39.42 -167.42 1 1.70e+01 3.46e-03 6.56e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1506 0.062 - 0.124: 172 0.124 - 0.185: 19 0.185 - 0.247: 7 0.247 - 0.309: 1 Chirality restraints: 1705 Sorted by residual: chirality pdb=" C3' U C 206 " pdb=" C4' U C 206 " pdb=" O3' U C 206 " pdb=" C2' U C 206 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' A C 78 " pdb=" C4' A C 78 " pdb=" O3' A C 78 " pdb=" C2' A C 78 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C3' A C 128 " pdb=" C4' A C 128 " pdb=" O3' A C 128 " pdb=" C2' A C 128 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1702 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 122 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.31e+00 pdb=" N9 A C 122 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A C 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A C 122 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 122 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 122 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 122 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 122 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A C 122 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 91 " -0.032 2.00e-02 2.50e+03 1.40e-02 5.86e+00 pdb=" N9 G C 91 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G C 91 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 91 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 91 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G C 91 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 127 " -0.030 2.00e-02 2.50e+03 1.56e-02 5.47e+00 pdb=" N1 C C 127 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C C 127 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C C 127 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 127 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C C 127 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C C 127 " 0.003 2.00e-02 2.50e+03 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 61 2.55 - 3.14: 6562 3.14 - 3.72: 16549 3.72 - 4.31: 23135 4.31 - 4.90: 32429 Nonbonded interactions: 78736 Sorted by model distance: nonbonded pdb=" ND1 HIS D 245 " pdb="MG MG D 501 " model vdw 1.962 2.250 nonbonded pdb=" NE2 HIS D 269 " pdb="MG MG D 501 " model vdw 2.018 2.250 nonbonded pdb=" OP2 DC E 111 " pdb="MG MG D 502 " model vdw 2.021 2.170 nonbonded pdb=" ND1 HIS D 273 " pdb="MG MG D 501 " model vdw 2.071 2.250 nonbonded pdb=" O2' U C 180 " pdb=" OP1 C C 181 " model vdw 2.127 3.040 ... (remaining 78731 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.007 0.340 9622 Z= 0.382 Angle : 0.712 7.704 14102 Z= 0.492 Chirality : 0.043 0.309 1705 Planarity : 0.004 0.053 938 Dihedral : 19.483 174.610 4308 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.37), residues: 492 helix: 0.82 (0.42), residues: 152 sheet: -1.55 (0.65), residues: 65 loop : -1.27 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.011 0.002 TYR D 340 PHE 0.007 0.001 PHE D 453 TRP 0.008 0.002 TRP D 478 HIS 0.007 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.36 ( 9620) covalent geometry : angle 0.71191 / 0.49 (14102) hydrogen bonds : bond 0.12252 / 7.93 ( 364) hydrogen bonds : angle 5.85488 / 4.00 ( 817) metal coordination : bond 0.24074 / 11.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.225 Fit side-chains REVERT: D 353 ASP cc_start: 0.7944 (m-30) cc_final: 0.7581 (p0) REVERT: D 403 ASP cc_start: 0.7861 (m-30) cc_final: 0.7354 (m-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1453 time to fit residues: 6.7344 Evaluate side-chains 27 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 212 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057661 restraints weight = 24484.279| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.70 r_work: 0.2796 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 9622 Z= 0.386 Angle : 0.765 11.887 14102 Z= 0.409 Chirality : 0.045 0.304 1705 Planarity : 0.006 0.074 938 Dihedral : 20.107 177.660 3306 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.71 % Allowed : 5.65 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.37), residues: 492 helix: 0.74 (0.42), residues: 152 sheet: -1.57 (0.63), residues: 65 loop : -1.31 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 375 TYR 0.011 0.002 TYR D 5 PHE 0.012 0.002 PHE D 453 TRP 0.008 0.002 TRP D 161 HIS 0.011 0.002 HIS D 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.39 ( 9620) covalent geometry : angle 0.76474 / 0.41 (14102) hydrogen bonds : bond 0.06585 / 4.32 ( 364) hydrogen bonds : angle 4.18124 / 2.89 ( 817) metal coordination : bond 0.00963 / 0.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.255 Fit side-chains REVERT: D 273 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7336 (t-170) REVERT: D 353 ASP cc_start: 0.8652 (m-30) cc_final: 0.7903 (p0) REVERT: D 403 ASP cc_start: 0.8380 (m-30) cc_final: 0.7533 (m-30) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.1360 time to fit residues: 5.3650 Evaluate side-chains 29 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060075 restraints weight = 24035.446| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.57 r_work: 0.2860 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9622 Z= 0.175 Angle : 0.622 10.027 14102 Z= 0.340 Chirality : 0.037 0.235 1705 Planarity : 0.004 0.045 938 Dihedral : 19.976 176.706 3306 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.18 % Allowed : 7.06 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.37), residues: 492 helix: 1.20 (0.42), residues: 152 sheet: -1.21 (0.65), residues: 61 loop : -1.05 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 155 TYR 0.011 0.001 TYR D 340 PHE 0.007 0.001 PHE D 198 TRP 0.006 0.001 TRP D 478 HIS 0.004 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 ( 9620) covalent geometry : angle 0.62174 / 0.34 (14102) hydrogen bonds : bond 0.05027 / 3.33 ( 364) hydrogen bonds : angle 3.82365 / 2.66 ( 817) metal coordination : bond 0.00453 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.218 Fit side-chains REVERT: D 208 ARG cc_start: 0.7486 (mpp80) cc_final: 0.6471 (mtp180) REVERT: D 353 ASP cc_start: 0.8639 (m-30) cc_final: 0.7931 (p0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.1345 time to fit residues: 6.3736 Evaluate side-chains 29 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.080430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058058 restraints weight = 24725.221| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.76 r_work: 0.2803 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9622 Z= 0.322 Angle : 0.697 10.950 14102 Z= 0.375 Chirality : 0.042 0.290 1705 Planarity : 0.005 0.040 938 Dihedral : 19.978 178.070 3306 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.65 % Allowed : 9.65 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.37), residues: 492 helix: 1.09 (0.42), residues: 152 sheet: -1.33 (0.64), residues: 60 loop : -1.20 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 101 TYR 0.013 0.002 TYR D 5 PHE 0.011 0.001 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.006 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.32 ( 9620) covalent geometry : angle 0.69657 / 0.38 (14102) hydrogen bonds : bond 0.05738 / 3.80 ( 364) hydrogen bonds : angle 3.83792 / 2.67 ( 817) metal coordination : bond 0.00199 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.137 Fit side-chains REVERT: D 208 ARG cc_start: 0.7583 (mpp80) cc_final: 0.6646 (mtp180) REVERT: D 273 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: D 353 ASP cc_start: 0.8691 (m-30) cc_final: 0.7968 (p0) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0837 time to fit residues: 3.9531 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058648 restraints weight = 24042.734| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.63 r_work: 0.2788 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9622 Z= 0.197 Angle : 0.623 10.161 14102 Z= 0.340 Chirality : 0.038 0.249 1705 Planarity : 0.004 0.040 938 Dihedral : 19.912 176.801 3306 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 10.59 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.37), residues: 492 helix: 1.26 (0.42), residues: 152 sheet: -1.25 (0.65), residues: 55 loop : -1.07 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 155 TYR 0.011 0.001 TYR D 484 PHE 0.007 0.001 PHE D 453 TRP 0.006 0.001 TRP D 478 HIS 0.008 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 ( 9620) covalent geometry : angle 0.62302 / 0.34 (14102) hydrogen bonds : bond 0.04934 / 3.27 ( 364) hydrogen bonds : angle 3.69509 / 2.59 ( 817) metal coordination : bond 0.00104 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.179 Fit side-chains REVERT: D 208 ARG cc_start: 0.7429 (mpp80) cc_final: 0.6398 (mtp180) REVERT: D 353 ASP cc_start: 0.8693 (m-30) cc_final: 0.8012 (p0) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0897 time to fit residues: 4.1438 Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056939 restraints weight = 23994.611| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.77 r_work: 0.2747 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 9622 Z= 0.347 Angle : 0.705 11.011 14102 Z= 0.379 Chirality : 0.042 0.302 1705 Planarity : 0.005 0.036 938 Dihedral : 19.928 177.390 3306 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.65 % Allowed : 11.53 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.37), residues: 492 helix: 1.03 (0.41), residues: 152 sheet: -1.20 (0.59), residues: 70 loop : -1.34 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 363 TYR 0.013 0.002 TYR D 5 PHE 0.012 0.002 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.005 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.35 ( 9620) covalent geometry : angle 0.70493 / 0.38 (14102) hydrogen bonds : bond 0.05715 / 3.81 ( 364) hydrogen bonds : angle 3.81497 / 2.65 ( 817) metal coordination : bond 0.00212 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.171 Fit side-chains REVERT: D 208 ARG cc_start: 0.7530 (mpp80) cc_final: 0.6571 (mtp180) REVERT: D 353 ASP cc_start: 0.8720 (m-30) cc_final: 0.8039 (p0) outliers start: 7 outliers final: 7 residues processed: 33 average time/residue: 0.1018 time to fit residues: 4.5055 Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.082131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059998 restraints weight = 23900.794| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.65 r_work: 0.2824 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9622 Z= 0.131 Angle : 0.596 9.333 14102 Z= 0.326 Chirality : 0.036 0.217 1705 Planarity : 0.004 0.039 938 Dihedral : 19.821 177.650 3306 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.41 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.37), residues: 492 helix: 1.37 (0.42), residues: 154 sheet: -1.19 (0.65), residues: 56 loop : -1.01 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.011 0.001 TYR D 340 PHE 0.007 0.001 PHE D 124 TRP 0.007 0.001 TRP D 478 HIS 0.025 0.002 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 ( 9620) covalent geometry : angle 0.59649 / 0.33 (14102) hydrogen bonds : bond 0.04425 / 2.97 ( 364) hydrogen bonds : angle 3.62970 / 2.54 ( 817) metal coordination : bond 0.00110 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.204 Fit side-chains REVERT: D 353 ASP cc_start: 0.8693 (m-30) cc_final: 0.8093 (p0) REVERT: D 389 MET cc_start: 0.8299 (tpp) cc_final: 0.7939 (tpp) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1063 time to fit residues: 4.7770 Evaluate side-chains 31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057806 restraints weight = 24085.705| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.76 r_work: 0.2769 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9622 Z= 0.281 Angle : 0.654 9.889 14102 Z= 0.353 Chirality : 0.040 0.262 1705 Planarity : 0.004 0.036 938 Dihedral : 19.802 178.607 3306 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.41 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.37), residues: 492 helix: 1.30 (0.42), residues: 152 sheet: -1.12 (0.64), residues: 60 loop : -1.08 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 363 TYR 0.012 0.002 TYR D 5 PHE 0.010 0.001 PHE D 453 TRP 0.005 0.001 TRP D 161 HIS 0.004 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.28 ( 9620) covalent geometry : angle 0.65362 / 0.35 (14102) hydrogen bonds : bond 0.05137 / 3.42 ( 364) hydrogen bonds : angle 3.69711 / 2.58 ( 817) metal coordination : bond 0.00159 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.150 Fit side-chains REVERT: D 353 ASP cc_start: 0.8675 (m-30) cc_final: 0.7857 (p0) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1099 time to fit residues: 4.8173 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057067 restraints weight = 24161.275| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.75 r_work: 0.2751 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9622 Z= 0.313 Angle : 0.681 10.455 14102 Z= 0.366 Chirality : 0.041 0.296 1705 Planarity : 0.005 0.036 938 Dihedral : 19.857 178.708 3306 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.41 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.37), residues: 492 helix: 1.11 (0.41), residues: 152 sheet: -1.05 (0.60), residues: 70 loop : -1.29 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 363 TYR 0.012 0.002 TYR D 5 PHE 0.011 0.001 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.004 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 ( 9620) covalent geometry : angle 0.68059 / 0.37 (14102) hydrogen bonds : bond 0.05419 / 3.62 ( 364) hydrogen bonds : angle 3.78679 / 2.66 ( 817) metal coordination : bond 0.00226 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.232 Fit side-chains REVERT: D 208 ARG cc_start: 0.7483 (mpp80) cc_final: 0.6555 (mtp180) REVERT: D 353 ASP cc_start: 0.8760 (m-30) cc_final: 0.7960 (p0) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.1135 time to fit residues: 5.4194 Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.080919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058748 restraints weight = 23816.324| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.64 r_work: 0.2793 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9622 Z= 0.192 Angle : 0.613 9.277 14102 Z= 0.333 Chirality : 0.037 0.245 1705 Planarity : 0.004 0.037 938 Dihedral : 19.750 178.917 3306 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.41 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.38), residues: 492 helix: 1.38 (0.42), residues: 152 sheet: -1.18 (0.67), residues: 55 loop : -0.99 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.011 0.001 TYR D 484 PHE 0.007 0.001 PHE D 79 TRP 0.008 0.001 TRP D 478 HIS 0.003 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 9620) covalent geometry : angle 0.61297 / 0.33 (14102) hydrogen bonds : bond 0.04644 / 3.11 ( 364) hydrogen bonds : angle 3.69095 / 2.59 ( 817) metal coordination : bond 0.00072 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: D 201 MET cc_start: 0.8626 (mtm) cc_final: 0.8166 (ttp) REVERT: D 208 ARG cc_start: 0.7369 (mpp80) cc_final: 0.6385 (mtp180) REVERT: D 353 ASP cc_start: 0.8756 (m-30) cc_final: 0.7948 (p0) outliers start: 6 outliers final: 6 residues processed: 33 average time/residue: 0.1074 time to fit residues: 4.7070 Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058452 restraints weight = 23560.925| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.64 r_work: 0.2786 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9622 Z= 0.227 Angle : 0.623 9.170 14102 Z= 0.338 Chirality : 0.038 0.249 1705 Planarity : 0.004 0.036 938 Dihedral : 19.725 179.368 3306 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.65 % Allowed : 10.82 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.37), residues: 492 helix: 1.31 (0.42), residues: 152 sheet: -1.19 (0.67), residues: 55 loop : -1.01 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 363 TYR 0.012 0.001 TYR D 484 PHE 0.008 0.001 PHE D 453 TRP 0.006 0.001 TRP D 478 HIS 0.009 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 ( 9620) covalent geometry : angle 0.62334 / 0.34 (14102) hydrogen bonds : bond 0.04737 / 3.17 ( 364) hydrogen bonds : angle 3.69056 / 2.59 ( 817) metal coordination : bond 0.00194 / 0.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.31 seconds wall clock time: 35 minutes 6.27 seconds (2106.27 seconds total)