Starting phenix.real_space_refine on Thu Jul 2 00:25:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2z_17380/07_2026/8p2z_17380.map" } resolution = 3.5 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 Cl 1 4.86 5 C 3073 2.51 5 N 712 2.21 5 O 824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 4641 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 199 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4404 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 552} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.21 Number of scatterers: 4641 At special positions: 0 Unit cell: (61.0785, 72.297, 103.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 31 16.00 O 824 8.00 N 712 7.00 C 3073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 358 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 701 " - " ASN C 131 " " NAG C 702 " - " ASN C 357 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 167.4 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 82.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 740 through 768 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.569A pdb=" N VAL C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.834A pdb=" N TYR C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Proline residue: C 46 - end of helix removed outlier: 3.666A pdb=" N VAL C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.610A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 4.030A pdb=" N SER C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 85 through 115 removed outlier: 3.645A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 167 through 188 removed outlier: 3.536A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.658A pdb=" N TYR C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 219 through 229 removed outlier: 4.129A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.758A pdb=" N TRP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.697A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.663A pdb=" N HIS C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.813A pdb=" N TYR C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.570A pdb=" N TRP C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 429 through 445 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.842A pdb=" N MET C 450 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.795A pdb=" N TRP C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 485 through 498 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 552 through 582 removed outlier: 3.640A pdb=" N LEU C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Proline residue: C 571 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 535 through 540 335 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.52 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: 990 1.33 - 1.45: 1152 1.45 - 1.57: 2573 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 4764 Sorted by residual: bond pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 1.231 1.305 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" CD YCP C 703 " pdb=" CE YCP C 703 " ideal model delta sigma weight residual 1.535 1.500 0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C YCP C 703 " pdb=" OXT YCP C 703 " ideal model delta sigma weight residual 1.246 1.214 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CB PRO C 353 " pdb=" CG PRO C 353 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.61e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 4759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6354 1.64 - 3.28: 131 3.28 - 4.92: 17 4.92 - 6.57: 5 6.57 - 8.21: 4 Bond angle restraints: 6511 Sorted by residual: angle pdb=" CA PRO C 353 " pdb=" N PRO C 353 " pdb=" CD PRO C 353 " ideal model delta sigma weight residual 112.00 103.84 8.16 1.40e+00 5.10e-01 3.40e+01 angle pdb=" CA YCP C 703 " pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 120.80 112.59 8.21 1.70e+00 3.46e-01 2.33e+01 angle pdb=" N LEU C 84 " pdb=" CA LEU C 84 " pdb=" C LEU C 84 " ideal model delta sigma weight residual 114.12 110.16 3.96 1.39e+00 5.18e-01 8.10e+00 angle pdb=" CB MET C 407 " pdb=" CG MET C 407 " pdb=" SD MET C 407 " ideal model delta sigma weight residual 112.70 105.37 7.33 3.00e+00 1.11e-01 5.97e+00 angle pdb=" CA LEU C 84 " pdb=" CB LEU C 84 " pdb=" CG LEU C 84 " ideal model delta sigma weight residual 116.30 124.06 -7.76 3.50e+00 8.16e-02 4.91e+00 ... (remaining 6506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 2462 18.06 - 36.12: 220 36.12 - 54.18: 53 54.18 - 72.24: 6 72.24 - 90.30: 4 Dihedral angle restraints: 2745 sinusoidal: 994 harmonic: 1751 Sorted by residual: dihedral pdb=" CA YCP C 703 " pdb=" N YCP C 703 " pdb=" CE YCP C 703 " pdb=" CD YCP C 703 " ideal model delta sinusoidal sigma weight residual 28.56 -61.74 90.30 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU C 267 " pdb=" CG GLU C 267 " pdb=" CD GLU C 267 " pdb=" OE1 GLU C 267 " ideal model delta sinusoidal sigma weight residual 0.00 87.41 -87.41 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA GLY C 511 " pdb=" C GLY C 511 " pdb=" N VAL C 512 " pdb=" CA VAL C 512 " ideal model delta harmonic sigma weight residual -180.00 -164.49 -15.51 0 5.00e+00 4.00e-02 9.62e+00 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 647 0.057 - 0.114: 115 0.114 - 0.171: 1 0.171 - 0.228: 0 0.228 - 0.285: 1 Chirality restraints: 764 Sorted by residual: chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 131 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA VAL C 368 " pdb=" N VAL C 368 " pdb=" C VAL C 368 " pdb=" CB VAL C 368 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" C PRO C 32 " pdb=" CB PRO C 32 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 761 not shown) Planarity restraints: 796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 352 " 0.094 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO C 353 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO C 353 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 353 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 365 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" CG ASP C 365 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP C 365 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP C 365 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 98 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LEU C 98 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU C 98 " 0.010 2.00e-02 2.50e+03 pdb=" N SER C 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 793 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 766 2.76 - 3.29: 4580 3.29 - 3.83: 8090 3.83 - 4.36: 8712 4.36 - 4.90: 15637 Nonbonded interactions: 37785 Sorted by model distance: nonbonded pdb=" OH TYR C 298 " pdb=" O LEU C 364 " model vdw 2.219 3.040 nonbonded pdb=" ND2 ASN C 27 " pdb=" OD1 ASN C 283 " model vdw 2.221 3.120 nonbonded pdb=" O ASP C 540 " pdb=" N GLY C 544 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR C 204 " pdb=" OG1 THR C 286 " model vdw 2.245 3.040 nonbonded pdb=" ND2 ASN C 27 " pdb=" OG SER C 287 " model vdw 2.271 3.120 ... (remaining 37780 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.560 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 4768 Z= 0.174 Angle : 0.630 8.207 6521 Z= 0.354 Chirality : 0.040 0.285 764 Planarity : 0.006 0.138 794 Dihedral : 14.807 90.304 1623 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.42 % Allowed : 17.65 % Favored : 81.93 % 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: 1.32 (0.35), residues: 598 helix: 1.64 (0.25), residues: 437 sheet: -0.24 (1.30), residues: 14 loop : -1.33 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.021 0.001 TYR C 21 PHE 0.013 0.001 PHE C 295 TRP 0.008 0.001 TRP C 178 HIS 0.001 0.000 HIS C 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4764) covalent geometry : angle 0.62028 / 0.35 ( 6511) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.72159 / 0.39 ( 4) hydrogen bonds : bond 0.14653 / 9.84 ( 335) hydrogen bonds : angle 6.22227 / 4.82 ( 999) link_NAG-ASN : bond 0.00385 / 0.20 ( 2) link_NAG-ASN : angle 3.60369 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.167 Fit side-chains REVERT: C 100 MET cc_start: 0.8359 (mtp) cc_final: 0.8141 (ttp) REVERT: C 271 ASN cc_start: 0.5772 (m-40) cc_final: 0.5401 (m-40) REVERT: C 407 MET cc_start: 0.9006 (tpp) cc_final: 0.8390 (mmm) REVERT: C 416 THR cc_start: 0.8660 (m) cc_final: 0.8332 (p) REVERT: C 568 MET cc_start: 0.7106 (ttm) cc_final: 0.6615 (ttt) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.0721 time to fit residues: 6.8526 Evaluate side-chains 63 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.0370 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 0.0070 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.1552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.165609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.139609 restraints weight = 5664.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143485 restraints weight = 3206.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.146027 restraints weight = 2250.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.147527 restraints weight = 1794.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.148708 restraints weight = 1556.843| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4768 Z= 0.112 Angle : 0.514 6.812 6521 Z= 0.260 Chirality : 0.039 0.274 764 Planarity : 0.004 0.079 794 Dihedral : 5.981 79.518 691 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.10 % Allowed : 15.34 % Favored : 82.56 % 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: 2.14 (0.35), residues: 598 helix: 2.19 (0.25), residues: 446 sheet: 0.68 (1.35), residues: 12 loop : -1.14 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 488 TYR 0.010 0.001 TYR C 463 PHE 0.010 0.001 PHE C 250 TRP 0.006 0.001 TRP C 178 HIS 0.002 0.001 HIS C 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 4764) covalent geometry : angle 0.50415 / 0.26 ( 6511) SS BOND : bond 0.00134 / 0.06 ( 2) SS BOND : angle 0.49683 / 0.29 ( 4) hydrogen bonds : bond 0.04265 / 2.74 ( 335) hydrogen bonds : angle 4.21039 / 3.03 ( 999) link_NAG-ASN : bond 0.00471 / 0.25 ( 2) link_NAG-ASN : angle 3.30957 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.160 Fit side-chains REVERT: C 70 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7422 (mmm-85) REVERT: C 84 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 271 ASN cc_start: 0.5669 (m-40) cc_final: 0.5322 (m-40) REVERT: C 365 ASP cc_start: 0.8466 (m-30) cc_final: 0.8240 (m-30) REVERT: C 385 MET cc_start: 0.7798 (mmt) cc_final: 0.7492 (mmm) REVERT: C 387 VAL cc_start: 0.7139 (OUTLIER) cc_final: 0.6707 (p) REVERT: C 416 THR cc_start: 0.8483 (m) cc_final: 0.8158 (p) REVERT: C 508 MET cc_start: 0.7053 (mmm) cc_final: 0.6473 (mmm) REVERT: C 521 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: C 568 MET cc_start: 0.7079 (ttm) cc_final: 0.6704 (ttt) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.0657 time to fit residues: 6.4650 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 45 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 GLN C 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.163166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136826 restraints weight = 5626.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140716 restraints weight = 3232.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.143034 restraints weight = 2282.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.144731 restraints weight = 1850.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.145810 restraints weight = 1596.358| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4768 Z= 0.112 Angle : 0.482 6.043 6521 Z= 0.242 Chirality : 0.039 0.265 764 Planarity : 0.004 0.062 794 Dihedral : 5.794 77.364 690 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.10 % Allowed : 15.55 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.34), residues: 598 helix: 2.33 (0.24), residues: 446 sheet: 0.64 (1.28), residues: 12 loop : -0.94 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 488 TYR 0.010 0.001 TYR C 101 PHE 0.011 0.001 PHE C 295 TRP 0.007 0.001 TRP C 111 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 4764) covalent geometry : angle 0.47385 / 0.24 ( 6511) SS BOND : bond 0.00070 / 0.04 ( 2) SS BOND : angle 0.49294 / 0.28 ( 4) hydrogen bonds : bond 0.03982 / 2.60 ( 335) hydrogen bonds : angle 3.98024 / 2.85 ( 999) link_NAG-ASN : bond 0.00443 / 0.23 ( 2) link_NAG-ASN : angle 2.98946 / 1.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.161 Fit side-chains REVERT: C 16 PHE cc_start: 0.7100 (m-80) cc_final: 0.6876 (m-80) REVERT: C 50 MET cc_start: 0.8002 (tpp) cc_final: 0.7793 (tpp) REVERT: C 70 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7322 (mtp180) REVERT: C 79 THR cc_start: 0.7399 (m) cc_final: 0.7055 (m) REVERT: C 365 ASP cc_start: 0.8401 (m-30) cc_final: 0.8139 (m-30) REVERT: C 387 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7039 (p) REVERT: C 508 MET cc_start: 0.7139 (mmm) cc_final: 0.6530 (mmm) REVERT: C 521 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: C 568 MET cc_start: 0.7018 (ttm) cc_final: 0.6656 (ttt) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.0634 time to fit residues: 5.8995 Evaluate side-chains 68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.0020 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 ASN C 543 GLN C 545 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.161299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134753 restraints weight = 5659.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138479 restraints weight = 3276.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140686 restraints weight = 2352.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.142330 restraints weight = 1921.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.143501 restraints weight = 1666.284| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4768 Z= 0.124 Angle : 0.488 6.060 6521 Z= 0.244 Chirality : 0.040 0.260 764 Planarity : 0.003 0.055 794 Dihedral : 5.774 76.693 690 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.31 % Allowed : 16.39 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.34), residues: 598 helix: 2.38 (0.24), residues: 446 sheet: 0.63 (1.27), residues: 12 loop : -0.82 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 68 TYR 0.012 0.001 TYR C 484 PHE 0.013 0.001 PHE C 295 TRP 0.008 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4764) covalent geometry : angle 0.48012 / 0.24 ( 6511) SS BOND : bond 0.00119 / 0.06 ( 2) SS BOND : angle 0.53371 / 0.31 ( 4) hydrogen bonds : bond 0.04016 / 2.64 ( 335) hydrogen bonds : angle 3.89926 / 2.79 ( 999) link_NAG-ASN : bond 0.00415 / 0.22 ( 2) link_NAG-ASN : angle 2.85540 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.130 Fit side-chains REVERT: A 750 MET cc_start: 0.7632 (tpp) cc_final: 0.7387 (tpp) REVERT: C 70 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7207 (mtp-110) REVERT: C 365 ASP cc_start: 0.8364 (m-30) cc_final: 0.7990 (m-30) REVERT: C 387 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7255 (p) REVERT: C 508 MET cc_start: 0.7236 (mmm) cc_final: 0.6579 (mmm) REVERT: C 521 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: C 568 MET cc_start: 0.7021 (ttm) cc_final: 0.6687 (ttt) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.0595 time to fit residues: 5.0872 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.159156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.132044 restraints weight = 5728.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135868 restraints weight = 3285.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138249 restraints weight = 2339.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.139928 restraints weight = 1888.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.140826 restraints weight = 1647.155| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4768 Z= 0.146 Angle : 0.507 6.032 6521 Z= 0.255 Chirality : 0.041 0.259 764 Planarity : 0.003 0.051 794 Dihedral : 5.817 76.379 690 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.34), residues: 598 helix: 2.40 (0.24), residues: 439 sheet: 0.78 (1.30), residues: 12 loop : -0.75 (0.52), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 488 TYR 0.010 0.001 TYR C 463 PHE 0.017 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.002 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4764) covalent geometry : angle 0.49980 / 0.25 ( 6511) SS BOND : bond 0.00154 / 0.08 ( 2) SS BOND : angle 0.76131 / 0.45 ( 4) hydrogen bonds : bond 0.04278 / 2.84 ( 335) hydrogen bonds : angle 3.91716 / 2.79 ( 999) link_NAG-ASN : bond 0.00373 / 0.20 ( 2) link_NAG-ASN : angle 2.87997 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7698 (tpp) cc_final: 0.7447 (tpp) REVERT: C 70 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7235 (mtp180) REVERT: C 183 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7571 (tp) REVERT: C 365 ASP cc_start: 0.8382 (m-30) cc_final: 0.7928 (m-30) REVERT: C 387 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7272 (p) REVERT: C 508 MET cc_start: 0.7046 (mmm) cc_final: 0.6521 (mmm) REVERT: C 521 PHE cc_start: 0.8210 (m-10) cc_final: 0.7913 (m-10) REVERT: C 568 MET cc_start: 0.7211 (ttm) cc_final: 0.6893 (ttt) outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.0516 time to fit residues: 4.5304 Evaluate side-chains 65 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.0060 chunk 54 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.160242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.133397 restraints weight = 5734.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.137203 restraints weight = 3261.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.139712 restraints weight = 2323.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.141124 restraints weight = 1862.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.142220 restraints weight = 1630.739| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4768 Z= 0.119 Angle : 0.479 5.766 6521 Z= 0.239 Chirality : 0.040 0.248 764 Planarity : 0.003 0.047 794 Dihedral : 5.739 76.607 690 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.15 % Allowed : 15.76 % Favored : 81.09 % 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: 2.60 (0.34), residues: 598 helix: 2.47 (0.24), residues: 442 sheet: 0.88 (1.35), residues: 12 loop : -0.64 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 488 TYR 0.011 0.001 TYR C 21 PHE 0.012 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 4764) covalent geometry : angle 0.47122 / 0.24 ( 6511) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.61899 / 0.36 ( 4) hydrogen bonds : bond 0.04003 / 2.66 ( 335) hydrogen bonds : angle 3.82616 / 2.72 ( 999) link_NAG-ASN : bond 0.00386 / 0.20 ( 2) link_NAG-ASN : angle 2.76322 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7684 (tpp) cc_final: 0.7443 (tpp) REVERT: C 70 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7245 (mtp180) REVERT: C 84 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 183 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7607 (tp) REVERT: C 271 ASN cc_start: 0.6187 (m-40) cc_final: 0.5958 (m-40) REVERT: C 365 ASP cc_start: 0.8340 (m-30) cc_final: 0.8065 (m-30) REVERT: C 387 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7280 (p) REVERT: C 508 MET cc_start: 0.7269 (mmm) cc_final: 0.6629 (mmm) REVERT: C 521 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: C 568 MET cc_start: 0.7223 (ttm) cc_final: 0.6904 (ttt) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 0.0599 time to fit residues: 5.1986 Evaluate side-chains 66 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 146 GLN C 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.159103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132389 restraints weight = 5723.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136160 restraints weight = 3325.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138405 restraints weight = 2377.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.140018 restraints weight = 1934.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140847 restraints weight = 1690.207| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4768 Z= 0.138 Angle : 0.501 5.932 6521 Z= 0.251 Chirality : 0.040 0.249 764 Planarity : 0.003 0.046 794 Dihedral : 5.793 76.668 690 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.73 % Allowed : 16.39 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.34), residues: 598 helix: 2.45 (0.23), residues: 439 sheet: 0.77 (1.34), residues: 12 loop : -0.73 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.012 0.001 TYR C 21 PHE 0.014 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.002 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4764) covalent geometry : angle 0.49464 / 0.25 ( 6511) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 0.60933 / 0.36 ( 4) hydrogen bonds : bond 0.04181 / 2.78 ( 335) hydrogen bonds : angle 3.86705 / 2.75 ( 999) link_NAG-ASN : bond 0.00374 / 0.20 ( 2) link_NAG-ASN : angle 2.72305 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7721 (tpp) cc_final: 0.7466 (tpp) REVERT: C 70 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7294 (mtp180) REVERT: C 84 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8092 (tt) REVERT: C 183 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7604 (tp) REVERT: C 365 ASP cc_start: 0.8326 (m-30) cc_final: 0.8005 (m-30) REVERT: C 387 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7286 (p) REVERT: C 508 MET cc_start: 0.7042 (mmm) cc_final: 0.6541 (mmm) REVERT: C 521 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: C 540 ASP cc_start: 0.7111 (t0) cc_final: 0.6643 (t0) REVERT: C 568 MET cc_start: 0.7238 (ttm) cc_final: 0.6960 (ttt) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.0621 time to fit residues: 5.8089 Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130393 restraints weight = 5789.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133971 restraints weight = 3282.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.136695 restraints weight = 2341.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138078 restraints weight = 1873.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.139153 restraints weight = 1639.502| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4768 Z= 0.138 Angle : 0.504 5.882 6521 Z= 0.253 Chirality : 0.040 0.245 764 Planarity : 0.003 0.044 794 Dihedral : 5.804 76.699 690 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.15 % Allowed : 16.81 % Favored : 80.04 % 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: 2.51 (0.34), residues: 598 helix: 2.46 (0.23), residues: 438 sheet: 0.89 (1.36), residues: 12 loop : -0.78 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 488 TYR 0.011 0.001 TYR C 21 PHE 0.014 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.002 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4764) covalent geometry : angle 0.49724 / 0.25 ( 6511) SS BOND : bond 0.00150 / 0.08 ( 2) SS BOND : angle 0.64711 / 0.38 ( 4) hydrogen bonds : bond 0.04214 / 2.80 ( 335) hydrogen bonds : angle 3.86502 / 2.75 ( 999) link_NAG-ASN : bond 0.00373 / 0.20 ( 2) link_NAG-ASN : angle 2.69328 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.128 Fit side-chains REVERT: A 750 MET cc_start: 0.7779 (tpp) cc_final: 0.7527 (tpp) REVERT: C 70 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7347 (mtp180) REVERT: C 84 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7989 (tt) REVERT: C 183 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (tp) REVERT: C 365 ASP cc_start: 0.8279 (m-30) cc_final: 0.7944 (m-30) REVERT: C 387 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7255 (p) REVERT: C 508 MET cc_start: 0.7043 (mmm) cc_final: 0.6527 (mmm) REVERT: C 521 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7891 (m-10) REVERT: C 540 ASP cc_start: 0.7116 (t0) cc_final: 0.6631 (t0) REVERT: C 568 MET cc_start: 0.7221 (ttm) cc_final: 0.6942 (ttt) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.0620 time to fit residues: 5.6426 Evaluate side-chains 72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.156732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129722 restraints weight = 5653.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.133501 restraints weight = 3239.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135890 restraints weight = 2304.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137378 restraints weight = 1866.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138175 restraints weight = 1632.836| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4768 Z= 0.149 Angle : 0.517 6.021 6521 Z= 0.259 Chirality : 0.041 0.243 764 Planarity : 0.003 0.044 794 Dihedral : 5.842 76.542 690 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.15 % Allowed : 16.60 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.34), residues: 598 helix: 2.42 (0.23), residues: 438 sheet: 0.81 (1.33), residues: 12 loop : -0.83 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 488 TYR 0.012 0.001 TYR C 21 PHE 0.015 0.001 PHE C 295 TRP 0.010 0.001 TRP C 111 HIS 0.002 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 4764) covalent geometry : angle 0.51041 / 0.26 ( 6511) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.69764 / 0.41 ( 4) hydrogen bonds : bond 0.04334 / 2.89 ( 335) hydrogen bonds : angle 3.89021 / 2.76 ( 999) link_NAG-ASN : bond 0.00356 / 0.19 ( 2) link_NAG-ASN : angle 2.68492 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7802 (tpp) cc_final: 0.7542 (tpp) REVERT: C 70 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7409 (mtp180) REVERT: C 84 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7879 (tt) REVERT: C 183 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7478 (tp) REVERT: C 365 ASP cc_start: 0.8269 (m-30) cc_final: 0.7918 (m-30) REVERT: C 387 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7255 (p) REVERT: C 508 MET cc_start: 0.7086 (mmm) cc_final: 0.6564 (mmm) REVERT: C 521 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: C 540 ASP cc_start: 0.7135 (t0) cc_final: 0.6646 (t0) REVERT: C 568 MET cc_start: 0.7219 (ttm) cc_final: 0.6912 (ttt) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.0617 time to fit residues: 5.7069 Evaluate side-chains 71 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.160059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.133088 restraints weight = 5662.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136722 restraints weight = 3281.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139098 restraints weight = 2373.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.140497 restraints weight = 1933.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141335 restraints weight = 1704.915| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4768 Z= 0.135 Angle : 0.503 5.921 6521 Z= 0.252 Chirality : 0.040 0.238 764 Planarity : 0.003 0.043 794 Dihedral : 5.792 76.600 690 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.36 % Allowed : 16.39 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.34), residues: 598 helix: 2.46 (0.23), residues: 439 sheet: 0.74 (1.32), residues: 12 loop : -0.81 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 488 TYR 0.012 0.001 TYR C 21 PHE 0.013 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4764) covalent geometry : angle 0.49710 / 0.25 ( 6511) SS BOND : bond 0.00133 / 0.07 ( 2) SS BOND : angle 0.60942 / 0.35 ( 4) hydrogen bonds : bond 0.04199 / 2.80 ( 335) hydrogen bonds : angle 3.85601 / 2.74 ( 999) link_NAG-ASN : bond 0.00359 / 0.19 ( 2) link_NAG-ASN : angle 2.65885 / 1.53 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7794 (tpp) cc_final: 0.7532 (tpp) REVERT: C 70 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7362 (mtp180) REVERT: C 183 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7501 (tp) REVERT: C 271 ASN cc_start: 0.6172 (m-40) cc_final: 0.5954 (m110) REVERT: C 365 ASP cc_start: 0.8253 (m-30) cc_final: 0.7908 (m-30) REVERT: C 387 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7309 (p) REVERT: C 508 MET cc_start: 0.7036 (mmm) cc_final: 0.6562 (mmm) REVERT: C 521 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: C 540 ASP cc_start: 0.7121 (t0) cc_final: 0.6645 (t0) REVERT: C 568 MET cc_start: 0.7165 (ttm) cc_final: 0.6904 (ttt) outliers start: 16 outliers final: 11 residues processed: 72 average time/residue: 0.0585 time to fit residues: 5.5244 Evaluate side-chains 72 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 521 PHE Chi-restraints excluded: chain C residue 569 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.160459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133358 restraints weight = 5752.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137073 restraints weight = 3332.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.139423 restraints weight = 2395.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140786 restraints weight = 1952.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.141914 restraints weight = 1723.823| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4768 Z= 0.136 Angle : 0.527 10.699 6521 Z= 0.258 Chirality : 0.040 0.235 764 Planarity : 0.003 0.043 794 Dihedral : 5.789 76.600 690 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.94 % Allowed : 17.02 % Favored : 80.04 % 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: 2.50 (0.34), residues: 598 helix: 2.46 (0.23), residues: 439 sheet: 0.78 (1.33), residues: 12 loop : -0.81 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 488 TYR 0.011 0.001 TYR C 21 PHE 0.013 0.001 PHE C 295 TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4764) covalent geometry : angle 0.52098 / 0.26 ( 6511) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 0.61604 / 0.36 ( 4) hydrogen bonds : bond 0.04212 / 2.80 ( 335) hydrogen bonds : angle 3.85689 / 2.74 ( 999) link_NAG-ASN : bond 0.00350 / 0.18 ( 2) link_NAG-ASN : angle 2.62509 / 1.51 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 767.57 seconds wall clock time: 13 minutes 57.14 seconds (837.14 seconds total)