Starting phenix.real_space_refine on Thu Nov 14 07:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_17380.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_17380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_17380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_17380.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2z_17380/11_2024/8p2z_17380.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} 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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.54, per 1000 atoms: 0.76 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: 1.33 Conformation dependent library (CDL) restraints added in 557.7 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: 0.50 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: 1.26 Time building geometry restraints manager: 1.46 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: 0.710 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 4764 Z= 0.242 Angle : 0.620 8.207 6511 Z= 0.353 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 178 HIS 0.001 0.000 HIS C 218 PHE 0.013 0.001 PHE C 295 TYR 0.021 0.001 TYR C 21 ARG 0.002 0.000 ARG C 78 *********************** 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 : 0.378 Fit side-chains REVERT: C 100 MET cc_start: 0.8359 (mtp) cc_final: 0.8139 (ttp) REVERT: C 271 ASN cc_start: 0.5772 (m-40) cc_final: 0.5402 (m-40) REVERT: C 407 MET cc_start: 0.9006 (tpp) cc_final: 0.8389 (mmm) REVERT: C 416 THR cc_start: 0.8660 (m) cc_final: 0.8331 (p) REVERT: C 568 MET cc_start: 0.7106 (ttm) cc_final: 0.6613 (ttt) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1933 time to fit residues: 17.7780 Evaluate side-chains 64 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4764 Z= 0.264 Angle : 0.557 6.326 6511 Z= 0.287 Chirality : 0.042 0.292 764 Planarity : 0.004 0.078 794 Dihedral : 6.231 79.930 691 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.52 % Allowed : 14.71 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 598 helix: 1.94 (0.24), residues: 442 sheet: 0.55 (1.34), residues: 12 loop : -1.28 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 178 HIS 0.002 0.001 HIS C 115 PHE 0.017 0.001 PHE C 295 TYR 0.015 0.001 TYR C 463 ARG 0.002 0.001 ARG C 488 *********************** 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 74 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.466 Fit side-chains REVERT: C 70 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7420 (mmm-85) REVERT: C 271 ASN cc_start: 0.5957 (m-40) cc_final: 0.5612 (m-40) REVERT: C 365 ASP cc_start: 0.8477 (m-30) cc_final: 0.8275 (m-30) REVERT: C 416 THR cc_start: 0.8576 (m) cc_final: 0.8301 (p) REVERT: C 508 MET cc_start: 0.7319 (mmm) cc_final: 0.6861 (mmm) REVERT: C 521 PHE cc_start: 0.8263 (m-10) cc_final: 0.8004 (m-10) REVERT: C 568 MET cc_start: 0.7088 (ttm) cc_final: 0.6644 (ttt) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.1724 time to fit residues: 16.4094 Evaluate side-chains 65 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 447 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN C 103 ASN C 247 GLN C 543 GLN C 545 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4764 Z= 0.163 Angle : 0.479 5.821 6511 Z= 0.245 Chirality : 0.039 0.273 764 Planarity : 0.004 0.061 794 Dihedral : 5.895 77.184 691 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.73 % Allowed : 14.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.34), residues: 598 helix: 2.15 (0.24), residues: 446 sheet: 0.56 (1.25), residues: 12 loop : -1.04 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 111 HIS 0.001 0.000 HIS C 275 PHE 0.011 0.001 PHE C 250 TYR 0.012 0.001 TYR C 21 ARG 0.006 0.001 ARG C 488 *********************** 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 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.490 Fit side-chains REVERT: C 16 PHE cc_start: 0.7228 (m-80) cc_final: 0.7004 (m-80) REVERT: C 70 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7487 (mmm-85) REVERT: C 365 ASP cc_start: 0.8417 (m-30) cc_final: 0.8188 (m-30) REVERT: C 387 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7167 (p) REVERT: C 508 MET cc_start: 0.7196 (mmm) cc_final: 0.6700 (mmm) REVERT: C 568 MET cc_start: 0.7167 (ttm) cc_final: 0.6764 (ttt) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.1697 time to fit residues: 16.1754 Evaluate side-chains 67 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 569 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4764 Z= 0.258 Angle : 0.533 6.098 6511 Z= 0.271 Chirality : 0.042 0.278 764 Planarity : 0.004 0.053 794 Dihedral : 5.986 76.608 690 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.78 % Allowed : 15.76 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.33), residues: 598 helix: 2.12 (0.24), residues: 436 sheet: 0.74 (1.28), residues: 12 loop : -1.02 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.002 0.001 HIS C 115 PHE 0.018 0.001 PHE C 295 TYR 0.015 0.001 TYR C 21 ARG 0.004 0.001 ARG C 488 *********************** 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 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: C 70 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7361 (mtp180) REVERT: C 508 MET cc_start: 0.7068 (mmm) cc_final: 0.6620 (mmm) REVERT: C 521 PHE cc_start: 0.8316 (m-10) cc_final: 0.7997 (m-10) REVERT: C 568 MET cc_start: 0.7282 (ttm) cc_final: 0.6833 (ttt) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.1701 time to fit residues: 15.7698 Evaluate side-chains 69 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 211 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 248 ILE 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 559 ILE Chi-restraints excluded: chain C residue 569 CYS Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4764 Z= 0.177 Angle : 0.485 5.748 6511 Z= 0.246 Chirality : 0.040 0.261 764 Planarity : 0.003 0.049 794 Dihedral : 5.851 76.497 690 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.94 % Allowed : 16.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.34), residues: 598 helix: 2.32 (0.24), residues: 438 sheet: 0.73 (1.30), residues: 12 loop : -0.84 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 PHE 0.011 0.001 PHE C 295 TYR 0.013 0.001 TYR C 21 ARG 0.003 0.000 ARG C 488 *********************** 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 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: C 70 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7320 (mtp180) REVERT: C 365 ASP cc_start: 0.8337 (m-30) cc_final: 0.8069 (m-30) REVERT: C 387 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (p) REVERT: C 508 MET cc_start: 0.7233 (mmm) cc_final: 0.6702 (mmm) REVERT: C 521 PHE cc_start: 0.8292 (m-10) cc_final: 0.7993 (m-10) REVERT: C 568 MET cc_start: 0.7178 (ttm) cc_final: 0.6794 (ttt) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.1702 time to fit residues: 16.0687 Evaluate side-chains 70 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 569 CYS Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4764 Z= 0.191 Angle : 0.484 5.878 6511 Z= 0.245 Chirality : 0.040 0.256 764 Planarity : 0.003 0.046 794 Dihedral : 5.815 76.534 690 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.36 % Allowed : 17.23 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.34), residues: 598 helix: 2.40 (0.24), residues: 437 sheet: 0.69 (1.31), residues: 12 loop : -0.86 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 PHE 0.012 0.001 PHE C 295 TYR 0.012 0.001 TYR C 21 ARG 0.003 0.000 ARG C 488 *********************** 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 78 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: C 70 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7325 (mtp180) REVERT: C 84 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8163 (tt) REVERT: C 271 ASN cc_start: 0.6223 (m-40) cc_final: 0.5994 (m-40) REVERT: C 365 ASP cc_start: 0.8311 (m-30) cc_final: 0.7981 (m-30) REVERT: C 387 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7322 (p) REVERT: C 508 MET cc_start: 0.7183 (mmm) cc_final: 0.6600 (mmm) REVERT: C 521 PHE cc_start: 0.8311 (m-10) cc_final: 0.8017 (m-10) REVERT: C 568 MET cc_start: 0.7146 (ttm) cc_final: 0.6820 (ttt) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1869 time to fit residues: 18.3028 Evaluate side-chains 76 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 ILE 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 569 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN C 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4764 Z= 0.204 Angle : 0.492 5.853 6511 Z= 0.249 Chirality : 0.040 0.253 764 Planarity : 0.003 0.045 794 Dihedral : 5.828 76.598 690 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.78 % Allowed : 16.60 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.33), residues: 598 helix: 2.38 (0.23), residues: 438 sheet: 0.68 (1.35), residues: 12 loop : -0.88 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 PHE 0.013 0.001 PHE C 295 TYR 0.012 0.001 TYR C 21 ARG 0.002 0.000 ARG C 488 *********************** 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 81 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.6926 (ttp) cc_final: 0.6653 (ttp) REVERT: C 70 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7305 (mtp180) REVERT: C 84 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 365 ASP cc_start: 0.8316 (m-30) cc_final: 0.7934 (m-30) REVERT: C 387 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7314 (p) REVERT: C 508 MET cc_start: 0.7184 (mmm) cc_final: 0.6606 (mmm) REVERT: C 515 LEU cc_start: 0.7848 (mm) cc_final: 0.7619 (mm) REVERT: C 521 PHE cc_start: 0.8286 (m-10) cc_final: 0.7982 (m-10) REVERT: C 568 MET cc_start: 0.7134 (ttm) cc_final: 0.6837 (ttt) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1694 time to fit residues: 17.2453 Evaluate side-chains 77 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 116 SER 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 569 CYS Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN C 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4764 Z= 0.209 Angle : 0.496 5.905 6511 Z= 0.252 Chirality : 0.040 0.249 764 Planarity : 0.003 0.044 794 Dihedral : 5.830 76.451 690 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.78 % Allowed : 16.81 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.33), residues: 598 helix: 2.48 (0.23), residues: 432 sheet: 0.82 (1.38), residues: 12 loop : -0.84 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 PHE 0.013 0.001 PHE C 295 TYR 0.013 0.001 TYR C 21 ARG 0.002 0.000 ARG C 68 *********************** 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 82 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.490 Fit side-chains REVERT: A 750 MET cc_start: 0.6948 (ttp) cc_final: 0.6667 (ttp) REVERT: C 70 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7396 (mtp180) REVERT: C 84 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7902 (tt) REVERT: C 365 ASP cc_start: 0.8336 (m-30) cc_final: 0.7924 (m-30) REVERT: C 387 VAL cc_start: 0.7506 (OUTLIER) cc_final: 0.7134 (p) REVERT: C 508 MET cc_start: 0.7196 (mmm) cc_final: 0.6623 (mmm) REVERT: C 515 LEU cc_start: 0.8041 (mm) cc_final: 0.7840 (mm) REVERT: C 521 PHE cc_start: 0.8288 (m-10) cc_final: 0.7975 (m-10) REVERT: C 540 ASP cc_start: 0.7183 (t0) cc_final: 0.6692 (t0) REVERT: C 568 MET cc_start: 0.7155 (ttm) cc_final: 0.6873 (ttt) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.1647 time to fit residues: 17.0401 Evaluate side-chains 80 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 ILE 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 569 CYS Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4764 Z= 0.222 Angle : 0.508 5.980 6511 Z= 0.257 Chirality : 0.041 0.248 764 Planarity : 0.003 0.043 794 Dihedral : 5.860 76.532 690 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.20 % Allowed : 16.81 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.33), residues: 598 helix: 2.44 (0.23), residues: 432 sheet: 0.80 (1.39), residues: 12 loop : -0.82 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.002 0.001 HIS C 115 PHE 0.014 0.001 PHE C 295 TYR 0.013 0.001 TYR C 21 ARG 0.003 0.000 ARG C 488 *********************** 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 84 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 750 MET cc_start: 0.7056 (ttp) cc_final: 0.6770 (ttp) REVERT: C 70 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7397 (mtp180) REVERT: C 84 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (tt) REVERT: C 271 ASN cc_start: 0.6239 (m-40) cc_final: 0.6011 (m110) REVERT: C 365 ASP cc_start: 0.8335 (m-30) cc_final: 0.8045 (m-30) REVERT: C 508 MET cc_start: 0.7028 (mmm) cc_final: 0.6620 (mmm) REVERT: C 521 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: C 540 ASP cc_start: 0.7214 (t0) cc_final: 0.6725 (t0) REVERT: C 568 MET cc_start: 0.7180 (ttm) cc_final: 0.6905 (ttt) outliers start: 20 outliers final: 17 residues processed: 81 average time/residue: 0.1684 time to fit residues: 17.7401 Evaluate side-chains 85 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 ILE 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 344 TYR 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 Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4764 Z= 0.214 Angle : 0.505 5.933 6511 Z= 0.255 Chirality : 0.040 0.244 764 Planarity : 0.003 0.042 794 Dihedral : 5.839 76.546 690 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.20 % Allowed : 16.81 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.33), residues: 598 helix: 2.39 (0.23), residues: 438 sheet: 0.82 (1.37), residues: 12 loop : -0.84 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS C 115 PHE 0.013 0.001 PHE C 295 TYR 0.012 0.001 TYR C 21 ARG 0.002 0.000 ARG C 488 ********************** 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 86 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.506 Fit side-chains REVERT: A 750 MET cc_start: 0.7036 (ttp) cc_final: 0.6737 (ttp) REVERT: C 70 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7383 (mtp180) REVERT: C 84 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7877 (tt) REVERT: C 361 GLU cc_start: 0.7276 (mp0) cc_final: 0.6910 (mp0) REVERT: C 365 ASP cc_start: 0.8291 (m-30) cc_final: 0.7863 (m-30) REVERT: C 508 MET cc_start: 0.7028 (mmm) cc_final: 0.6622 (mmm) REVERT: C 521 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7923 (m-10) REVERT: C 540 ASP cc_start: 0.7179 (t0) cc_final: 0.6704 (t0) REVERT: C 568 MET cc_start: 0.7182 (ttm) cc_final: 0.6926 (ttt) outliers start: 20 outliers final: 18 residues processed: 83 average time/residue: 0.1707 time to fit residues: 18.4574 Evaluate side-chains 84 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 116 SER 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 344 TYR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 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 561 LEU Chi-restraints excluded: chain C residue 569 CYS Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.159428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132308 restraints weight = 5610.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136005 restraints weight = 3264.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138457 restraints weight = 2353.040| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4764 Z= 0.227 Angle : 0.514 6.006 6511 Z= 0.260 Chirality : 0.041 0.242 764 Planarity : 0.003 0.042 794 Dihedral : 5.871 76.538 690 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.41 % Allowed : 16.60 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.33), residues: 598 helix: 2.36 (0.23), residues: 437 sheet: 0.80 (1.37), residues: 12 loop : -0.88 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.002 0.001 HIS C 115 PHE 0.013 0.001 PHE C 295 TYR 0.012 0.001 TYR C 21 ARG 0.002 0.000 ARG C 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.03 seconds wall clock time: 24 minutes 2.10 seconds (1442.10 seconds total)