Starting phenix.real_space_refine on Wed Aug 5 02:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hr_75700/08_2026/11hr_75700.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 200 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 4305 2.51 5 N 1511 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3817 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 20, 'TRANS': 455} Chain breaks: 2 Chain: "B" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 3970 Classifications: {'RNA': 185} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 63} Link IDs: {'rna2p': 30, 'rna3p': 154} Chain breaks: 1 Chain: "D" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 298 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" 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 1765 SG CYS A 234 19.180 32.649 83.542 1.00409.21 S ATOM 1790 SG CYS A 237 17.616 33.342 85.902 1.00411.61 S ATOM 1969 SG CYS A 265 15.982 30.806 84.010 1.00418.52 S Time building chain proxies: 1.86, per 1000 atoms: 0.23 Number of scatterers: 8088 At special positions: 0 Unit cell: (104.775, 110.55, 127.05, 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 23 16.00 P 200 15.00 Mg 2 11.99 O 2046 8.00 N 1511 7.00 C 4305 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: 0.66 Conformation dependent library (CDL) restraints added in 283.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" ND1 HIS A 268 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 237 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 265 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 234 " Number of angles added : 3 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 38.7% alpha, 15.8% beta 71 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.602A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 163 through 182 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.721A pdb=" N ARG A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 314 removed outlier: 4.488A pdb=" N VAL A 298 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.900A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 461 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.362A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 41 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.385A pdb=" N THR A 321 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 191 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A 55 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 192 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 79 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR A 72 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 77 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 380 removed outlier: 7.089A pdb=" N GLN A 432 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.616A pdb=" N TYR A 387 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.675A pdb=" N ILE A 444 " --> pdb=" O LEU A 485 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1449 1.33 - 1.45: 3045 1.45 - 1.57: 3738 1.57 - 1.69: 397 1.69 - 1.80: 37 Bond restraints: 8666 Sorted by residual: bond pdb=" C4' DC D 10 " pdb=" C3' DC D 10 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.18e+00 bond pdb=" C3' DT D 7 " pdb=" O3' DT D 7 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.60e+00 bond pdb=" C3' DC D 8 " pdb=" O3' DC D 8 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.53e+00 bond pdb=" C4' DC D 8 " pdb=" C3' DC D 8 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.00e-02 1.00e+04 5.16e+00 bond pdb=" N9 A B 193 " pdb=" C4 A B 193 " ideal model delta sigma weight residual 1.374 1.361 0.013 6.00e-03 2.78e+04 5.01e+00 ... (remaining 8661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 11866 1.57 - 3.14: 732 3.14 - 4.71: 48 4.71 - 6.28: 8 6.28 - 7.85: 1 Bond angle restraints: 12655 Sorted by residual: angle pdb=" C1' U B 229 " pdb=" N1 U B 229 " pdb=" C2 U B 229 " ideal model delta sigma weight residual 117.70 125.55 -7.85 1.20e+00 6.94e-01 4.28e+01 angle pdb=" O4' DC D 2 " pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " ideal model delta sigma weight residual 106.00 102.37 3.63 6.00e-01 2.78e+00 3.67e+01 angle pdb=" N1 U B 97 " pdb=" C2 U B 97 " pdb=" O2 U B 97 " ideal model delta sigma weight residual 122.80 127.03 -4.23 7.00e-01 2.04e+00 3.65e+01 angle pdb=" N1 U B 229 " pdb=" C2 U B 229 " pdb=" O2 U B 229 " ideal model delta sigma weight residual 122.80 126.90 -4.10 7.00e-01 2.04e+00 3.43e+01 angle pdb=" O2 C B 219 " pdb=" C2 C B 219 " pdb=" N3 C B 219 " ideal model delta sigma weight residual 121.90 117.93 3.97 7.00e-01 2.04e+00 3.22e+01 ... (remaining 12650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 4909 35.34 - 70.68: 425 70.68 - 106.02: 48 106.02 - 141.37: 5 141.37 - 176.71: 5 Dihedral angle restraints: 5392 sinusoidal: 4008 harmonic: 1384 Sorted by residual: dihedral pdb=" O4' C B 49 " pdb=" C1' C B 49 " pdb=" N1 C B 49 " pdb=" C2 C B 49 " ideal model delta sinusoidal sigma weight residual 200.00 38.36 161.64 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' C B 83 " pdb=" C1' C B 83 " pdb=" N1 C B 83 " pdb=" C2 C B 83 " ideal model delta sinusoidal sigma weight residual -128.00 48.71 -176.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 96 " pdb=" C1' U B 96 " pdb=" N1 U B 96 " pdb=" C2 U B 96 " ideal model delta sinusoidal sigma weight residual -128.00 27.06 -155.06 1 1.70e+01 3.46e-03 6.33e+01 ... (remaining 5389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1133 0.046 - 0.091: 198 0.091 - 0.137: 192 0.137 - 0.182: 22 0.182 - 0.228: 1 Chirality restraints: 1546 Sorted by residual: chirality pdb=" C3' A B 86 " pdb=" C4' A B 86 " pdb=" O3' A B 86 " pdb=" C2' A B 86 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' G B 7 " pdb=" O4' G B 7 " pdb=" C2' G B 7 " pdb=" N9 G B 7 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" C3' DA D 9 " pdb=" C4' DA D 9 " pdb=" O3' DA D 9 " pdb=" C2' DA D 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1543 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 80 " -0.026 2.00e-02 2.50e+03 1.14e-02 3.91e+00 pdb=" N9 G B 80 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G B 80 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 80 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 80 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 80 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 80 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 80 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 7 " -0.024 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 7 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 7 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 7 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G B 7 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " 0.022 2.00e-02 2.50e+03 9.99e-03 2.74e+00 pdb=" N9 A B 56 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 56 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 56 " -0.003 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 72 2.61 - 3.18: 6740 3.18 - 3.75: 15947 3.75 - 4.33: 20614 4.33 - 4.90: 28930 Nonbonded interactions: 72303 Sorted by model distance: nonbonded pdb=" OE2 GLU A 192 " pdb="MG MG A 501 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP A 60 " pdb="MG MG A 501 " model vdw 2.256 2.170 nonbonded pdb=" NE2 HIS A 273 " pdb="MG MG A 502 " model vdw 2.468 2.250 nonbonded pdb=" CB HIS A 245 " pdb="MG MG A 502 " model vdw 2.476 2.570 nonbonded pdb=" CD2 HIS A 269 " pdb="MG MG A 502 " model vdw 2.503 2.390 ... (remaining 72298 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.030 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.005 0.053 8670 Z= 0.405 Angle : 0.810 33.485 12658 Z= 0.630 Chirality : 0.055 0.228 1546 Planarity : 0.003 0.024 873 Dihedral : 21.618 176.707 4498 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.39), residues: 470 helix: 1.22 (0.41), residues: 170 sheet: -1.33 (0.63), residues: 75 loop : -0.58 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.010 0.001 TYR A 5 PHE 0.013 0.001 PHE A 40 TRP 0.004 0.001 TRP A 161 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.41 ( 8666) covalent geometry : angle 0.74704 / 0.62 (12655) hydrogen bonds : bond 0.08471 / 6.05 ( 350) hydrogen bonds : angle 4.34829 / 2.90 ( 803) metal coordination : bond 0.03090 / 1.55 ( 4) metal coordination : angle 20.42819 / 11.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.121 Fit side-chains REVERT: A 92 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7943 (mttm) REVERT: A 147 ASN cc_start: 0.8482 (p0) cc_final: 0.8181 (p0) REVERT: A 228 MET cc_start: 0.7439 (mmm) cc_final: 0.7206 (ptp) REVERT: A 402 MET cc_start: 0.8246 (tpp) cc_final: 0.7823 (tpp) REVERT: A 432 GLN cc_start: 0.8841 (mt0) cc_final: 0.8622 (mt0) REVERT: A 467 ASN cc_start: 0.8136 (m-40) cc_final: 0.7847 (m-40) outliers start: 0 outliers final: 1 residues processed: 107 average time/residue: 0.5261 time to fit residues: 59.7685 Evaluate side-chains 57 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.0070 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 2.3860 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.101914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066561 restraints weight = 19656.311| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.66 r_work: 0.2903 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8670 Z= 0.276 Angle : 0.734 7.851 12658 Z= 0.413 Chirality : 0.044 0.314 1546 Planarity : 0.006 0.052 873 Dihedral : 22.882 176.392 3515 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.90 % Allowed : 13.53 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.38), residues: 470 helix: 0.42 (0.39), residues: 170 sheet: -1.29 (0.68), residues: 63 loop : -0.84 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 155 TYR 0.032 0.003 TYR A 340 PHE 0.021 0.003 PHE A 40 TRP 0.011 0.002 TRP A 478 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.28 ( 8666) covalent geometry : angle 0.73295 / 0.41 (12655) hydrogen bonds : bond 0.06871 / 4.81 ( 350) hydrogen bonds : angle 3.95709 / 2.68 ( 803) metal coordination : bond 0.00664 / 0.35 ( 4) metal coordination : angle 2.74816 / 1.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8494 (mmpt) cc_final: 0.8293 (mmpt) REVERT: A 92 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8138 (mttp) REVERT: A 159 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8894 (tptp) REVERT: A 228 MET cc_start: 0.7625 (mmm) cc_final: 0.7344 (ptp) REVERT: A 339 HIS cc_start: 0.8884 (t70) cc_final: 0.8639 (t70) REVERT: A 371 ARG cc_start: 0.9145 (ptm160) cc_final: 0.8872 (ttm-80) REVERT: A 432 GLN cc_start: 0.8851 (mt0) cc_final: 0.8622 (mt0) REVERT: A 467 ASN cc_start: 0.8258 (m-40) cc_final: 0.7978 (m-40) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.5282 time to fit residues: 43.3907 Evaluate side-chains 65 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.100456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064026 restraints weight = 19683.663| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.68 r_work: 0.2849 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8670 Z= 0.246 Angle : 0.654 12.369 12658 Z= 0.367 Chirality : 0.043 0.301 1546 Planarity : 0.007 0.125 873 Dihedral : 22.834 176.650 3515 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.66 % Allowed : 17.15 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.38), residues: 470 helix: 0.50 (0.38), residues: 171 sheet: -1.49 (0.67), residues: 68 loop : -0.74 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 457 TYR 0.021 0.002 TYR A 340 PHE 0.025 0.003 PHE A 79 TRP 0.010 0.002 TRP A 161 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.25 ( 8666) covalent geometry : angle 0.64366 / 0.37 (12655) hydrogen bonds : bond 0.06464 / 4.51 ( 350) hydrogen bonds : angle 4.00067 / 2.80 ( 803) metal coordination : bond 0.00960 / 0.48 ( 4) metal coordination : angle 7.49416 / 4.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8393 (mttm) REVERT: A 159 LYS cc_start: 0.9333 (mtpt) cc_final: 0.9013 (tppt) REVERT: A 184 LEU cc_start: 0.9044 (mt) cc_final: 0.8802 (mm) REVERT: A 339 HIS cc_start: 0.8759 (t70) cc_final: 0.8510 (t70) REVERT: A 432 GLN cc_start: 0.8833 (mt0) cc_final: 0.8603 (mt0) REVERT: A 467 ASN cc_start: 0.8417 (m-40) cc_final: 0.8050 (m-40) REVERT: A 478 TRP cc_start: 0.8428 (t-100) cc_final: 0.8204 (t-100) REVERT: A 481 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9150 (mmmm) outliers start: 11 outliers final: 3 residues processed: 66 average time/residue: 0.5762 time to fit residues: 40.3465 Evaluate side-chains 58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.101376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065224 restraints weight = 19997.648| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.81 r_work: 0.2886 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8670 Z= 0.135 Angle : 0.518 7.748 12658 Z= 0.301 Chirality : 0.035 0.290 1546 Planarity : 0.004 0.050 873 Dihedral : 22.871 177.958 3513 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.17 % Allowed : 20.53 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.39), residues: 470 helix: 0.94 (0.39), residues: 171 sheet: -1.37 (0.66), residues: 68 loop : -0.64 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 195 TYR 0.016 0.001 TYR A 344 PHE 0.022 0.002 PHE A 329 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 ( 8666) covalent geometry : angle 0.51692 / 0.30 (12655) hydrogen bonds : bond 0.05711 / 3.94 ( 350) hydrogen bonds : angle 3.72743 / 2.53 ( 803) metal coordination : bond 0.00470 / 0.24 ( 4) metal coordination : angle 1.94891 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8445 (mttm) REVERT: A 159 LYS cc_start: 0.9317 (mtpt) cc_final: 0.9053 (tppt) REVERT: A 339 HIS cc_start: 0.8853 (t70) cc_final: 0.8577 (t70) REVERT: A 432 GLN cc_start: 0.8871 (mt0) cc_final: 0.8666 (mt0) REVERT: A 467 ASN cc_start: 0.8373 (m-40) cc_final: 0.7970 (m-40) REVERT: A 478 TRP cc_start: 0.8571 (t-100) cc_final: 0.8302 (t-100) REVERT: A 481 LYS cc_start: 0.9406 (mmmm) cc_final: 0.9182 (mmmm) outliers start: 9 outliers final: 2 residues processed: 66 average time/residue: 0.5361 time to fit residues: 37.3750 Evaluate side-chains 54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062883 restraints weight = 19798.505| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.68 r_work: 0.2829 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8670 Z= 0.210 Angle : 0.581 6.774 12658 Z= 0.332 Chirality : 0.039 0.318 1546 Planarity : 0.005 0.034 873 Dihedral : 22.737 176.215 3513 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.90 % Allowed : 20.77 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.38), residues: 470 helix: 1.02 (0.40), residues: 171 sheet: -1.33 (0.64), residues: 68 loop : -0.62 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 327 TYR 0.014 0.002 TYR A 46 PHE 0.017 0.002 PHE A 79 TRP 0.003 0.001 TRP A 478 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 ( 8666) covalent geometry : angle 0.57943 / 0.33 (12655) hydrogen bonds : bond 0.06144 / 4.26 ( 350) hydrogen bonds : angle 3.77569 / 2.60 ( 803) metal coordination : bond 0.00477 / 0.24 ( 4) metal coordination : angle 2.75500 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8572 (mttm) REVERT: A 159 LYS cc_start: 0.9347 (mtpt) cc_final: 0.9076 (tppt) REVERT: A 296 LEU cc_start: 0.8221 (tp) cc_final: 0.8020 (tm) REVERT: A 327 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7851 (ptp90) REVERT: A 339 HIS cc_start: 0.8701 (t70) cc_final: 0.8421 (t70) REVERT: A 363 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7928 (ptm160) REVERT: A 467 ASN cc_start: 0.8409 (m-40) cc_final: 0.8159 (m-40) REVERT: A 481 LYS cc_start: 0.9433 (mmmm) cc_final: 0.9188 (mmmm) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.5859 time to fit residues: 37.9732 Evaluate side-chains 52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.100404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064291 restraints weight = 19420.984| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.80 r_work: 0.2865 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8670 Z= 0.143 Angle : 0.556 11.513 12658 Z= 0.312 Chirality : 0.036 0.286 1546 Planarity : 0.004 0.026 873 Dihedral : 22.809 177.726 3513 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.21 % Allowed : 23.19 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.38), residues: 470 helix: 1.10 (0.40), residues: 170 sheet: -0.97 (0.65), residues: 62 loop : -0.72 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.023 0.001 TYR A 344 PHE 0.015 0.001 PHE A 40 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 8666) covalent geometry : angle 0.54261 / 0.31 (12655) hydrogen bonds : bond 0.05525 / 3.83 ( 350) hydrogen bonds : angle 3.83726 / 2.65 ( 803) metal coordination : bond 0.01676 / 0.86 ( 4) metal coordination : angle 7.81602 / 4.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: A 92 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8536 (mttm) REVERT: A 159 LYS cc_start: 0.9328 (mtpt) cc_final: 0.9106 (tppt) REVERT: A 296 LEU cc_start: 0.8232 (tp) cc_final: 0.8021 (tm) REVERT: A 327 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7852 (ptp90) REVERT: A 329 PHE cc_start: 0.8395 (t80) cc_final: 0.8185 (t80) REVERT: A 339 HIS cc_start: 0.8539 (t70) cc_final: 0.8223 (t70) REVERT: A 481 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9183 (mmmm) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.6094 time to fit residues: 33.7041 Evaluate side-chains 54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.096818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061527 restraints weight = 19396.041| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.52 r_work: 0.2786 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8670 Z= 0.266 Angle : 0.659 9.674 12658 Z= 0.365 Chirality : 0.044 0.376 1546 Planarity : 0.005 0.034 873 Dihedral : 22.706 175.984 3513 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.14 % Allowed : 22.22 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.38), residues: 470 helix: 0.86 (0.40), residues: 170 sheet: -1.14 (0.61), residues: 72 loop : -0.86 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.015 0.002 TYR A 340 PHE 0.022 0.002 PHE A 314 TRP 0.004 0.001 TRP A 161 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.27 ( 8666) covalent geometry : angle 0.65000 / 0.36 (12655) hydrogen bonds : bond 0.06631 / 4.64 ( 350) hydrogen bonds : angle 4.06060 / 2.85 ( 803) metal coordination : bond 0.01250 / 0.65 ( 4) metal coordination : angle 7.18448 / 3.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: A 159 LYS cc_start: 0.9334 (mtpt) cc_final: 0.9102 (tppt) REVERT: A 296 LEU cc_start: 0.8444 (tp) cc_final: 0.8161 (tm) REVERT: A 339 HIS cc_start: 0.8458 (t70) cc_final: 0.8205 (t70) REVERT: A 344 TYR cc_start: 0.8455 (t80) cc_final: 0.8122 (t80) REVERT: A 481 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9177 (mmmm) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.5224 time to fit residues: 32.9516 Evaluate side-chains 56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 482 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.099651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063517 restraints weight = 19526.003| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.69 r_work: 0.2844 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8670 Z= 0.137 Angle : 0.563 11.337 12658 Z= 0.318 Chirality : 0.035 0.293 1546 Planarity : 0.004 0.045 873 Dihedral : 22.825 177.971 3513 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 25.12 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.38), residues: 470 helix: 1.02 (0.41), residues: 170 sheet: -0.83 (0.61), residues: 70 loop : -0.72 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 33 TYR 0.012 0.001 TYR A 344 PHE 0.015 0.002 PHE A 40 TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 ( 8666) covalent geometry : angle 0.55556 / 0.32 (12655) hydrogen bonds : bond 0.05592 / 3.89 ( 350) hydrogen bonds : angle 3.94705 / 2.76 ( 803) metal coordination : bond 0.01239 / 0.63 ( 4) metal coordination : angle 6.06276 / 3.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 69 SER cc_start: 0.7783 (t) cc_final: 0.7503 (m) REVERT: A 159 LYS cc_start: 0.9306 (mtpt) cc_final: 0.9074 (tppt) REVERT: A 296 LEU cc_start: 0.8412 (tp) cc_final: 0.8142 (tm) REVERT: A 339 HIS cc_start: 0.8468 (t70) cc_final: 0.8210 (t70) REVERT: A 344 TYR cc_start: 0.8433 (t80) cc_final: 0.8130 (t80) REVERT: A 481 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9172 (mmmm) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.5786 time to fit residues: 36.2551 Evaluate side-chains 52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.097871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062524 restraints weight = 19145.130| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.54 r_work: 0.2811 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8670 Z= 0.205 Angle : 0.609 12.514 12658 Z= 0.335 Chirality : 0.039 0.314 1546 Planarity : 0.004 0.043 873 Dihedral : 22.722 177.019 3513 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.17 % Allowed : 24.64 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.38), residues: 470 helix: 0.93 (0.41), residues: 170 sheet: -0.43 (0.63), residues: 64 loop : -0.80 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 413 TYR 0.016 0.002 TYR A 340 PHE 0.017 0.002 PHE A 314 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 ( 8666) covalent geometry : angle 0.60195 / 0.33 (12655) hydrogen bonds : bond 0.05851 / 4.06 ( 350) hydrogen bonds : angle 3.94432 / 2.76 ( 803) metal coordination : bond 0.01150 / 0.59 ( 4) metal coordination : angle 5.95527 / 3.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: A 159 LYS cc_start: 0.9300 (mtpt) cc_final: 0.9080 (tppt) REVERT: A 296 LEU cc_start: 0.8467 (tp) cc_final: 0.8165 (tm) REVERT: A 339 HIS cc_start: 0.8434 (t70) cc_final: 0.8170 (t70) REVERT: A 344 TYR cc_start: 0.8462 (t80) cc_final: 0.8242 (t80) REVERT: A 481 LYS cc_start: 0.9437 (mmmm) cc_final: 0.9168 (mmmm) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.5516 time to fit residues: 34.0809 Evaluate side-chains 52 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.098131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.061438 restraints weight = 19518.686| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.81 r_work: 0.2805 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8670 Z= 0.198 Angle : 0.626 12.396 12658 Z= 0.340 Chirality : 0.038 0.309 1546 Planarity : 0.004 0.033 873 Dihedral : 22.759 177.364 3513 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.45 % Allowed : 26.81 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.38), residues: 470 helix: 0.84 (0.40), residues: 170 sheet: -0.70 (0.60), residues: 70 loop : -0.71 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 330 TYR 0.013 0.001 TYR A 344 PHE 0.015 0.002 PHE A 79 TRP 0.004 0.001 TRP A 478 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 ( 8666) covalent geometry : angle 0.61985 / 0.34 (12655) hydrogen bonds : bond 0.05687 / 3.97 ( 350) hydrogen bonds : angle 3.99435 / 2.79 ( 803) metal coordination : bond 0.01077 / 0.56 ( 4) metal coordination : angle 5.73006 / 3.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8550 (mpp) cc_final: 0.8208 (mmm) REVERT: A 76 GLU cc_start: 0.8535 (pp20) cc_final: 0.8318 (pm20) REVERT: A 84 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: A 159 LYS cc_start: 0.9298 (mtpt) cc_final: 0.9078 (tppt) REVERT: A 339 HIS cc_start: 0.8372 (t70) cc_final: 0.8110 (t70) REVERT: A 481 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9160 (mmmm) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.5244 time to fit residues: 28.8631 Evaluate side-chains 53 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.096958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060357 restraints weight = 19609.299| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.73 r_work: 0.2777 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8670 Z= 0.230 Angle : 0.639 11.580 12658 Z= 0.350 Chirality : 0.040 0.336 1546 Planarity : 0.004 0.032 873 Dihedral : 22.733 177.021 3513 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.93 % Allowed : 26.09 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.38), residues: 470 helix: 0.82 (0.40), residues: 170 sheet: -0.84 (0.59), residues: 70 loop : -0.80 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 327 TYR 0.017 0.002 TYR A 344 PHE 0.016 0.002 PHE A 79 TRP 0.002 0.001 TRP A 478 HIS 0.008 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 ( 8666) covalent geometry : angle 0.63264 / 0.35 (12655) hydrogen bonds : bond 0.06088 / 4.26 ( 350) hydrogen bonds : angle 4.07316 / 2.85 ( 803) metal coordination : bond 0.01056 / 0.55 ( 4) metal coordination : angle 5.74917 / 3.22 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2912.22 seconds wall clock time: 50 minutes 21.17 seconds (3021.17 seconds total)