Starting phenix.real_space_refine on Thu Jul 2 09:55:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hr_75700/07_2026/11hr_75700.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hr_75700/07_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_75700/07_2026/11hr_75700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hr_75700/07_2026/11hr_75700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hr_75700/07_2026/11hr_75700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hr_75700/07_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-dev-6108/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: 1.34, per 1000 atoms: 0.17 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: 0.52 Conformation dependent library (CDL) restraints added in 172.6 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: 0.81 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: 1.02 Time building geometry restraints manager: 0.66 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: 12347 1.57 - 3.14: 262 3.14 - 4.71: 37 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: 1327 0.046 - 0.091: 165 0.091 - 0.137: 50 0.137 - 0.182: 3 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=" 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 chirality pdb=" C1' U B 229 " pdb=" O4' U B 229 " pdb=" C2' U B 229 " pdb=" N1 U B 229 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.97e-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: 1.260 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.780 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: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- 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= 0.380 Angle : 0.650 33.485 12658 Z= 0.510 Chirality : 0.035 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 0.00449 / 0.38 ( 8666) covalent geometry : angle 0.56895 / 0.50 (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 : 0.115 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: 0.7812 (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: 0.3758 time to fit residues: 42.8788 Evaluate side-chains 56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 2.2040 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.102263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066565 restraints weight = 19756.998| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.77 r_work: 0.2909 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8670 Z= 0.267 Angle : 0.736 10.152 12658 Z= 0.407 Chirality : 0.042 0.322 1546 Planarity : 0.006 0.058 873 Dihedral : 22.877 175.430 3515 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.66 % Allowed : 13.29 % Favored : 84.06 % 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: -0.75 (0.38), residues: 470 helix: 0.43 (0.39), residues: 171 sheet: -1.35 (0.66), residues: 63 loop : -0.88 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 457 TYR 0.027 0.003 TYR A 5 PHE 0.027 0.003 PHE A 79 TRP 0.011 0.003 TRP A 478 HIS 0.008 0.002 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.27 ( 8666) covalent geometry : angle 0.73432 / 0.41 (12655) hydrogen bonds : bond 0.06595 / 4.55 ( 350) hydrogen bonds : angle 3.94632 / 2.67 ( 803) metal coordination : bond 0.01332 / 0.67 ( 4) metal coordination : angle 3.16774 / 1.70 ( 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 78 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8117 (mttm) REVERT: A 159 LYS cc_start: 0.9016 (tptp) cc_final: 0.8743 (tptt) REVERT: A 184 LEU cc_start: 0.8787 (mt) cc_final: 0.8572 (mm) REVERT: A 228 MET cc_start: 0.7638 (mmm) cc_final: 0.7354 (ptp) REVERT: A 339 HIS cc_start: 0.8891 (t70) cc_final: 0.8635 (t70) REVERT: A 432 GLN cc_start: 0.8858 (mt0) cc_final: 0.8622 (mt0) REVERT: A 467 ASN cc_start: 0.8265 (m-40) cc_final: 0.7997 (m-40) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.3980 time to fit residues: 31.8639 Evaluate side-chains 67 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 83 LEU 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: 20.0000 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.101145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065143 restraints weight = 19487.791| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.68 r_work: 0.2871 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8670 Z= 0.224 Angle : 0.568 11.558 12658 Z= 0.333 Chirality : 0.039 0.266 1546 Planarity : 0.006 0.131 873 Dihedral : 22.834 176.114 3515 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 18.84 % Favored : 79.23 % 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: 0.76 (0.39), residues: 171 sheet: -1.40 (0.66), residues: 68 loop : -0.70 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 457 TYR 0.015 0.002 TYR A 340 PHE 0.022 0.003 PHE A 79 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 8666) covalent geometry : angle 0.55779 / 0.33 (12655) hydrogen bonds : bond 0.06004 / 4.19 ( 350) hydrogen bonds : angle 3.93547 / 2.74 ( 803) metal coordination : bond 0.00905 / 0.45 ( 4) metal coordination : angle 6.96517 / 4.06 ( 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 63 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8278 (mttp) REVERT: A 159 LYS cc_start: 0.9188 (tptp) cc_final: 0.8868 (tptt) REVERT: A 184 LEU cc_start: 0.8945 (mt) cc_final: 0.8736 (mm) REVERT: A 228 MET cc_start: 0.7640 (mmm) cc_final: 0.7365 (ptp) REVERT: A 339 HIS cc_start: 0.8784 (t70) cc_final: 0.8552 (t70) REVERT: A 467 ASN cc_start: 0.8508 (m-40) cc_final: 0.8213 (m-40) REVERT: A 481 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9048 (mmmm) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 0.4281 time to fit residues: 28.1908 Evaluate side-chains 56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 303 ILE 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: 2.9990 chunk 42 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.100701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065383 restraints weight = 19762.328| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.64 r_work: 0.2880 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8670 Z= 0.174 Angle : 0.521 7.000 12658 Z= 0.307 Chirality : 0.036 0.288 1546 Planarity : 0.004 0.046 873 Dihedral : 22.830 176.278 3515 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 20.53 % Favored : 76.81 % 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: -0.25 (0.38), residues: 470 helix: 1.08 (0.40), residues: 171 sheet: -1.31 (0.66), residues: 63 loop : -0.71 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.014 0.001 TYR A 305 PHE 0.022 0.003 PHE A 329 TRP 0.008 0.001 TRP A 478 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 ( 8666) covalent geometry : angle 0.51997 / 0.31 (12655) hydrogen bonds : bond 0.05551 / 3.80 ( 350) hydrogen bonds : angle 3.69645 / 2.53 ( 803) metal coordination : bond 0.00326 / 0.17 ( 4) metal coordination : angle 1.67712 / 0.97 ( 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 69 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (pp) REVERT: A 92 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8310 (mttp) REVERT: A 159 LYS cc_start: 0.9237 (tptp) cc_final: 0.8943 (tptt) REVERT: A 339 HIS cc_start: 0.8845 (t70) cc_final: 0.8553 (t70) REVERT: A 467 ASN cc_start: 0.8438 (m-40) cc_final: 0.8144 (m-40) REVERT: A 481 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9132 (mmmm) outliers start: 11 outliers final: 3 residues processed: 64 average time/residue: 0.4347 time to fit residues: 29.5050 Evaluate side-chains 60 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 186 VAL 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: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 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 = 0.3726 r_free = 0.3726 target = 0.101258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065239 restraints weight = 19819.200| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.70 r_work: 0.2884 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8670 Z= 0.147 Angle : 0.499 7.146 12658 Z= 0.295 Chirality : 0.035 0.258 1546 Planarity : 0.004 0.059 873 Dihedral : 22.801 176.635 3513 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 22.46 % 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: -0.04 (0.39), residues: 470 helix: 1.29 (0.40), residues: 171 sheet: -1.09 (0.65), residues: 64 loop : -0.65 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.016 0.001 TYR A 344 PHE 0.015 0.002 PHE A 79 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 8666) covalent geometry : angle 0.49791 / 0.30 (12655) hydrogen bonds : bond 0.05282 / 3.67 ( 350) hydrogen bonds : angle 3.65566 / 2.52 ( 803) metal coordination : bond 0.00405 / 0.20 ( 4) metal coordination : angle 2.55076 / 1.50 ( 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 62 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7867 (ptm-80) cc_final: 0.7631 (ptm160) REVERT: A 89 ASP cc_start: 0.8573 (t0) cc_final: 0.8304 (t0) REVERT: A 92 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8428 (mttm) REVERT: A 159 LYS cc_start: 0.9275 (tptp) cc_final: 0.8955 (tptt) REVERT: A 339 HIS cc_start: 0.8814 (t70) cc_final: 0.8523 (t70) REVERT: A 467 ASN cc_start: 0.8446 (m-40) cc_final: 0.8161 (m-40) REVERT: A 481 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9128 (mmmm) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.4699 time to fit residues: 30.3453 Evaluate side-chains 56 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.064987 restraints weight = 19448.061| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.77 r_work: 0.2880 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8670 Z= 0.155 Angle : 0.521 8.504 12658 Z= 0.296 Chirality : 0.036 0.261 1546 Planarity : 0.004 0.048 873 Dihedral : 22.757 176.470 3513 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 24.15 % Favored : 74.15 % 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: 0.09 (0.39), residues: 470 helix: 1.45 (0.41), residues: 172 sheet: -0.89 (0.66), residues: 64 loop : -0.68 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 480 TYR 0.020 0.002 TYR A 340 PHE 0.023 0.003 PHE A 314 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 8666) covalent geometry : angle 0.51001 / 0.29 (12655) hydrogen bonds : bond 0.05199 / 3.58 ( 350) hydrogen bonds : angle 3.64661 / 2.53 ( 803) metal coordination : bond 0.02564 / 1.33 ( 4) metal coordination : angle 6.78148 / 3.64 ( 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 61 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8058 (ptm-80) cc_final: 0.7781 (ptm160) REVERT: A 89 ASP cc_start: 0.8518 (t0) cc_final: 0.8224 (t0) REVERT: A 92 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8496 (mttm) REVERT: A 159 LYS cc_start: 0.9299 (tptp) cc_final: 0.8988 (tptt) REVERT: A 339 HIS cc_start: 0.8753 (t70) cc_final: 0.8437 (t70) REVERT: A 481 LYS cc_start: 0.9392 (mmmm) cc_final: 0.9150 (mmmm) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.5433 time to fit residues: 34.4647 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.099421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063074 restraints weight = 19622.202| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.82 r_work: 0.2839 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8670 Z= 0.203 Angle : 0.577 11.523 12658 Z= 0.324 Chirality : 0.037 0.278 1546 Planarity : 0.006 0.113 873 Dihedral : 22.720 175.990 3513 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.90 % Allowed : 25.12 % 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: -0.04 (0.39), residues: 470 helix: 1.16 (0.40), residues: 170 sheet: -0.95 (0.63), residues: 64 loop : -0.59 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 330 TYR 0.036 0.002 TYR A 344 PHE 0.016 0.002 PHE A 79 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 ( 8666) covalent geometry : angle 0.56596 / 0.32 (12655) hydrogen bonds : bond 0.05463 / 3.78 ( 350) hydrogen bonds : angle 3.85893 / 2.71 ( 803) metal coordination : bond 0.01290 / 0.67 ( 4) metal coordination : angle 7.19876 / 3.96 ( 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 60 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: A 89 ASP cc_start: 0.8584 (t0) cc_final: 0.8265 (t0) REVERT: A 92 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8532 (mttm) REVERT: A 159 LYS cc_start: 0.9293 (tptp) cc_final: 0.8954 (tptt) REVERT: A 296 LEU cc_start: 0.8258 (tp) cc_final: 0.8050 (tm) REVERT: A 329 PHE cc_start: 0.8585 (t80) cc_final: 0.8236 (t80) REVERT: A 339 HIS cc_start: 0.8574 (t70) cc_final: 0.8265 (t70) REVERT: A 480 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8508 (mtp85) REVERT: A 481 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9141 (mmmm) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 0.4819 time to fit residues: 28.2826 Evaluate side-chains 55 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 367 VAL 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: 3.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.099601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063195 restraints weight = 19439.100| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.80 r_work: 0.2839 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8670 Z= 0.183 Angle : 0.570 10.878 12658 Z= 0.319 Chirality : 0.036 0.274 1546 Planarity : 0.004 0.056 873 Dihedral : 22.746 176.589 3513 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.69 % Allowed : 26.09 % Favored : 72.22 % 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: -0.04 (0.39), residues: 470 helix: 1.13 (0.41), residues: 170 sheet: -0.95 (0.62), residues: 68 loop : -0.54 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 480 TYR 0.023 0.002 TYR A 340 PHE 0.017 0.002 PHE A 314 TRP 0.004 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 8666) covalent geometry : angle 0.56320 / 0.32 (12655) hydrogen bonds : bond 0.05325 / 3.69 ( 350) hydrogen bonds : angle 3.92789 / 2.77 ( 803) metal coordination : bond 0.01101 / 0.57 ( 4) metal coordination : angle 5.80133 / 3.18 ( 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 : 0.196 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8749 (mtpp) REVERT: A 25 ILE cc_start: 0.9431 (tt) cc_final: 0.9201 (mt) REVERT: A 69 SER cc_start: 0.7696 (t) cc_final: 0.7422 (m) REVERT: A 84 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 89 ASP cc_start: 0.8545 (t0) cc_final: 0.8246 (t0) REVERT: A 92 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8556 (mppt) REVERT: A 159 LYS cc_start: 0.9298 (tptp) cc_final: 0.8949 (tptt) REVERT: A 296 LEU cc_start: 0.8332 (tp) cc_final: 0.8085 (tm) REVERT: A 329 PHE cc_start: 0.8596 (t80) cc_final: 0.8256 (t80) REVERT: A 339 HIS cc_start: 0.8534 (t70) cc_final: 0.8212 (t70) REVERT: A 344 TYR cc_start: 0.8295 (t80) cc_final: 0.8078 (t80) REVERT: A 480 ARG cc_start: 0.8977 (ttm110) cc_final: 0.8531 (mtp85) REVERT: A 481 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9152 (mmmm) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.4931 time to fit residues: 31.3359 Evaluate side-chains 58 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064677 restraints weight = 19339.880| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.70 r_work: 0.2873 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8670 Z= 0.146 Angle : 0.571 12.311 12658 Z= 0.317 Chirality : 0.035 0.256 1546 Planarity : 0.004 0.062 873 Dihedral : 22.755 177.132 3513 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.69 % Allowed : 27.05 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.39), residues: 470 helix: 1.11 (0.40), residues: 172 sheet: -0.71 (0.64), residues: 68 loop : -0.51 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.014 0.001 TYR A 344 PHE 0.013 0.002 PHE A 79 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 8666) covalent geometry : angle 0.56408 / 0.32 (12655) hydrogen bonds : bond 0.05130 / 3.54 ( 350) hydrogen bonds : angle 3.83554 / 2.70 ( 803) metal coordination : bond 0.01139 / 0.58 ( 4) metal coordination : angle 5.83322 / 3.24 ( 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: 7 poor density : 54 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.8639 (mpp) cc_final: 0.8415 (mmm) REVERT: A 25 ILE cc_start: 0.9459 (tt) cc_final: 0.9238 (mt) REVERT: A 69 SER cc_start: 0.7666 (t) cc_final: 0.7378 (m) REVERT: A 84 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: A 89 ASP cc_start: 0.8458 (t0) cc_final: 0.8129 (t0) REVERT: A 92 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8487 (mttm) REVERT: A 159 LYS cc_start: 0.9300 (tptp) cc_final: 0.8929 (tptt) REVERT: A 296 LEU cc_start: 0.8355 (tp) cc_final: 0.8095 (tm) REVERT: A 329 PHE cc_start: 0.8589 (t80) cc_final: 0.8220 (t80) REVERT: A 339 HIS cc_start: 0.8504 (t70) cc_final: 0.8195 (t70) REVERT: A 480 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8547 (mtp85) REVERT: A 481 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9151 (mmmm) outliers start: 7 outliers final: 7 residues processed: 59 average time/residue: 0.4661 time to fit residues: 29.2812 Evaluate side-chains 60 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 367 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: 20.0000 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.099293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063899 restraints weight = 19319.117| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.64 r_work: 0.2845 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8670 Z= 0.203 Angle : 0.602 12.257 12658 Z= 0.330 Chirality : 0.036 0.267 1546 Planarity : 0.004 0.070 873 Dihedral : 22.707 176.579 3513 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 27.29 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.39), residues: 470 helix: 1.09 (0.40), residues: 172 sheet: -0.76 (0.63), residues: 68 loop : -0.52 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.017 0.002 TYR A 340 PHE 0.015 0.002 PHE A 79 TRP 0.003 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 ( 8666) covalent geometry : angle 0.59533 / 0.33 (12655) hydrogen bonds : bond 0.05328 / 3.67 ( 350) hydrogen bonds : angle 3.87072 / 2.73 ( 803) metal coordination : bond 0.01079 / 0.56 ( 4) metal coordination : angle 5.66410 / 3.15 ( 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 59 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9484 (tt) cc_final: 0.9271 (mt) REVERT: A 69 SER cc_start: 0.7781 (t) cc_final: 0.7472 (m) REVERT: A 84 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: A 89 ASP cc_start: 0.8479 (t0) cc_final: 0.8132 (t0) REVERT: A 92 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8558 (mppt) REVERT: A 159 LYS cc_start: 0.9301 (tptp) cc_final: 0.8933 (tptt) REVERT: A 296 LEU cc_start: 0.8405 (tp) cc_final: 0.8151 (tm) REVERT: A 329 PHE cc_start: 0.8616 (t80) cc_final: 0.8229 (t80) REVERT: A 339 HIS cc_start: 0.8507 (t70) cc_final: 0.8244 (t70) REVERT: A 480 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8563 (mtp85) REVERT: A 481 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9149 (mmmm) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.4918 time to fit residues: 29.7262 Evaluate side-chains 59 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 367 VAL 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: 0.9980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 3 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065255 restraints weight = 19635.417| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.80 r_work: 0.2893 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8670 Z= 0.127 Angle : 0.553 11.544 12658 Z= 0.308 Chirality : 0.034 0.233 1546 Planarity : 0.004 0.055 873 Dihedral : 22.764 177.555 3513 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.93 % Allowed : 27.05 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.39), residues: 470 helix: 1.17 (0.41), residues: 172 sheet: -0.56 (0.64), residues: 68 loop : -0.50 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.029 0.002 TYR A 344 PHE 0.012 0.001 PHE A 40 TRP 0.007 0.001 TRP A 478 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 8666) covalent geometry : angle 0.54684 / 0.31 (12655) hydrogen bonds : bond 0.05043 / 3.49 ( 350) hydrogen bonds : angle 3.81421 / 2.69 ( 803) metal coordination : bond 0.01034 / 0.53 ( 4) metal coordination : angle 5.34781 / 2.98 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.31 seconds wall clock time: 42 minutes 1.80 seconds (2521.80 seconds total)