Starting phenix.real_space_refine on Tue Aug 4 21:00:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij3_60614/08_2026/9ij3_60614.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 51 5.49 5 S 43 5.16 5 C 4284 2.51 5 N 1211 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7005 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5921 Classifications: {'peptide': 738} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 702} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 533 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 12} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.25 Number of scatterers: 7005 At special positions: 0 Unit cell: (75.24, 84.36, 107.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 43 16.00 P 51 15.00 O 1415 8.00 N 1211 7.00 C 4284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 353.6 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 34.8% alpha, 15.9% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.763A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.505A pdb=" N SER A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 628 Processing helix chain 'A' and resid 646 through 661 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.948A pdb=" N GLY A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 703' Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.691A pdb=" N LYS A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 914 through 928 Processing helix chain 'A' and resid 939 through 955 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.772A pdb=" N TYR A 859 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 564 through 565 removed outlier: 4.549A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AB3, first strand: chain 'A' and resid 667 through 671 258 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1099 1.32 - 1.45: 2147 1.45 - 1.57: 3849 1.57 - 1.70: 100 1.70 - 1.82: 67 Bond restraints: 7262 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" C SER A 816 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C SER A 816 " pdb=" O SER A 816 " ideal model delta sigma weight residual 1.234 1.198 0.037 1.21e-02 6.83e+03 9.13e+00 bond pdb=" N GLN A 819 " pdb=" CA GLN A 819 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.06e-02 8.90e+03 9.09e+00 bond pdb=" C GLN A 819 " pdb=" O GLN A 819 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.39e-02 5.18e+03 8.50e+00 bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.66e-02 3.63e+03 7.14e+00 ... (remaining 7257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 9955 3.40 - 6.80: 100 6.80 - 10.20: 15 10.20 - 13.61: 6 13.61 - 17.01: 3 Bond angle restraints: 10079 Sorted by residual: angle pdb=" N GLY A 818 " pdb=" CA GLY A 818 " pdb=" C GLY A 818 " ideal model delta sigma weight residual 115.63 104.00 11.63 1.49e+00 4.50e-01 6.09e+01 angle pdb=" N GLN A 819 " pdb=" CA GLN A 819 " pdb=" C GLN A 819 " ideal model delta sigma weight residual 113.19 101.25 11.94 1.58e+00 4.01e-01 5.71e+01 angle pdb=" N1 C B 11 " pdb=" C6 C B 11 " pdb=" C5 C B 11 " ideal model delta sigma weight residual 121.00 124.07 -3.07 5.00e-01 4.00e+00 3.77e+01 angle pdb=" C1' C B 24 " pdb=" N1 C B 24 " pdb=" C2 C B 24 " ideal model delta sigma weight residual 118.80 125.14 -6.34 1.10e+00 8.26e-01 3.33e+01 angle pdb=" CB MET A 613 " pdb=" CG MET A 613 " pdb=" SD MET A 613 " ideal model delta sigma weight residual 112.70 129.71 -17.01 3.00e+00 1.11e-01 3.21e+01 ... (remaining 10074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3636 17.98 - 35.97: 503 35.97 - 53.95: 185 53.95 - 71.93: 82 71.93 - 89.92: 24 Dihedral angle restraints: 4430 sinusoidal: 2269 harmonic: 2161 Sorted by residual: dihedral pdb=" CA ILE A 415 " pdb=" C ILE A 415 " pdb=" N VAL A 416 " pdb=" CA VAL A 416 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C4' U B 7 " pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" C2' U B 7 " ideal model delta sinusoidal sigma weight residual 3.00 -30.45 33.45 1 8.00e+00 1.56e-02 2.49e+01 dihedral pdb=" CA TRP A 639 " pdb=" C TRP A 639 " pdb=" N VAL A 640 " pdb=" CA VAL A 640 " ideal model delta harmonic sigma weight residual 180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 4427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 967 0.077 - 0.154: 207 0.154 - 0.230: 10 0.230 - 0.307: 1 0.307 - 0.384: 1 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CB ILE A 357 " pdb=" CA ILE A 357 " pdb=" CG1 ILE A 357 " pdb=" CG2 ILE A 357 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C3' A C 14 " pdb=" C4' A C 14 " pdb=" O3' A C 14 " pdb=" C2' A C 14 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB THR A 548 " pdb=" CA THR A 548 " pdb=" OG1 THR A 548 " pdb=" CG2 THR A 548 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1183 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 358 " 0.037 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 358 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A 358 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 358 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 358 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 358 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 358 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 358 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 628 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO A 629 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 472 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C HIS A 472 " -0.050 2.00e-02 2.50e+03 pdb=" O HIS A 472 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 473 " 0.017 2.00e-02 2.50e+03 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 52 2.55 - 3.14: 4985 3.14 - 3.73: 12225 3.73 - 4.31: 17046 4.31 - 4.90: 26182 Nonbonded interactions: 60490 Sorted by model distance: nonbonded pdb=" OD1 ASP A 743 " pdb="MN MN A1001 " model vdw 1.968 2.320 nonbonded pdb=" CE LYS A 252 " pdb=" OP1 U C 11 " model vdw 2.122 3.440 nonbonded pdb=" OD2 ASP A 369 " pdb=" OG1 THR A 880 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 249 " pdb=" NH1 ARG A 255 " model vdw 2.319 3.120 nonbonded pdb=" OH TYR A 904 " pdb=" O ARG A 937 " model vdw 2.322 3.040 ... (remaining 60485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.200 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7262 Z= 0.266 Angle : 1.023 17.007 10079 Z= 0.621 Chirality : 0.059 0.384 1186 Planarity : 0.007 0.076 1085 Dihedral : 20.447 89.918 3030 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.77 % Favored : 91.10 % Rotamer: Outliers : 1.20 % Allowed : 31.38 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.04 (0.29), residues: 730 helix: -0.75 (0.32), residues: 226 sheet: -1.22 (0.40), residues: 159 loop : -1.77 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.031 0.003 TYR A 425 PHE 0.016 0.002 PHE A 758 TRP 0.070 0.003 TRP A 358 HIS 0.009 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.27 ( 7262) covalent geometry : angle 1.02300 / 0.62 (10079) hydrogen bonds : bond 0.14615 / 10.04 ( 312) hydrogen bonds : angle 7.07774 / 5.14 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 831 LEU cc_start: 0.5188 (tp) cc_final: 0.4924 (tp) outliers start: 8 outliers final: 4 residues processed: 103 average time/residue: 0.4489 time to fit residues: 49.2582 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 591 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS A 958 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.217731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179487 restraints weight = 7350.197| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 1.70 r_work: 0.4181 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4084 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7262 Z= 0.247 Angle : 0.777 9.571 10079 Z= 0.400 Chirality : 0.049 0.158 1186 Planarity : 0.006 0.066 1085 Dihedral : 17.382 79.472 1568 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.61 % Allowed : 28.98 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.84 (0.30), residues: 730 helix: -0.17 (0.34), residues: 232 sheet: -1.36 (0.40), residues: 146 loop : -1.85 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 937 TYR 0.013 0.003 TYR A 888 PHE 0.017 0.002 PHE A 758 TRP 0.036 0.003 TRP A 358 HIS 0.010 0.002 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 ( 7262) covalent geometry : angle 0.77744 / 0.40 (10079) hydrogen bonds : bond 0.05951 / 4.08 ( 312) hydrogen bonds : angle 5.71564 / 4.04 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5739 (mp) REVERT: A 228 LEU cc_start: 0.3198 (OUTLIER) cc_final: 0.2533 (mt) REVERT: A 276 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 329 MET cc_start: 0.7591 (tpp) cc_final: 0.7216 (mpp) REVERT: A 623 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.6016 (mt) REVERT: A 831 LEU cc_start: 0.6319 (tp) cc_final: 0.6090 (tp) outliers start: 44 outliers final: 20 residues processed: 112 average time/residue: 0.4018 time to fit residues: 48.2084 Evaluate side-chains 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 905 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.215659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.177425 restraints weight = 7298.340| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.69 r_work: 0.4176 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7262 Z= 0.231 Angle : 0.760 9.826 10079 Z= 0.390 Chirality : 0.048 0.233 1186 Planarity : 0.006 0.061 1085 Dihedral : 17.386 78.035 1566 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.96 % Allowed : 28.53 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.76 (0.30), residues: 730 helix: -0.01 (0.34), residues: 232 sheet: -1.42 (0.40), residues: 137 loop : -1.83 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.011 0.002 TYR A 241 PHE 0.016 0.002 PHE A 325 TRP 0.030 0.002 TRP A 358 HIS 0.008 0.002 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 ( 7262) covalent geometry : angle 0.76006 / 0.39 (10079) hydrogen bonds : bond 0.05650 / 3.82 ( 312) hydrogen bonds : angle 5.64736 / 3.99 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.2892 (mt) REVERT: A 254 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6461 (ttm) REVERT: A 276 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7151 (mt) REVERT: A 329 MET cc_start: 0.7680 (tpp) cc_final: 0.7101 (mpp) REVERT: A 623 LEU cc_start: 0.6525 (mm) cc_final: 0.6113 (mt) REVERT: A 624 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: A 671 ILE cc_start: 0.4464 (OUTLIER) cc_final: 0.3710 (tp) REVERT: A 672 MET cc_start: 0.5433 (mmp) cc_final: 0.5115 (mmt) REVERT: A 918 MET cc_start: 0.5819 (ptp) cc_final: 0.5551 (ptm) outliers start: 53 outliers final: 18 residues processed: 124 average time/residue: 0.3451 time to fit residues: 46.1216 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.218815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.181077 restraints weight = 7431.481| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 1.71 r_work: 0.4209 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7262 Z= 0.153 Angle : 0.667 11.874 10079 Z= 0.342 Chirality : 0.044 0.196 1186 Planarity : 0.005 0.060 1085 Dihedral : 17.207 79.856 1564 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.04 % Favored : 90.82 % Rotamer: Outliers : 5.26 % Allowed : 30.18 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.68 (0.30), residues: 730 helix: 0.22 (0.34), residues: 232 sheet: -1.65 (0.37), residues: 142 loop : -1.77 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.013 0.002 TYR A 321 PHE 0.012 0.001 PHE A 272 TRP 0.028 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 7262) covalent geometry : angle 0.66712 / 0.34 (10079) hydrogen bonds : bond 0.04551 / 3.08 ( 312) hydrogen bonds : angle 5.41009 / 3.83 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.3067 (mt) REVERT: A 254 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6406 (ttm) REVERT: A 276 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6968 (mt) REVERT: A 623 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6086 (mt) REVERT: A 671 ILE cc_start: 0.4076 (OUTLIER) cc_final: 0.3446 (tp) REVERT: A 672 MET cc_start: 0.5451 (mmp) cc_final: 0.5205 (mmt) REVERT: A 924 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7162 (mttt) outliers start: 35 outliers final: 16 residues processed: 110 average time/residue: 0.4059 time to fit residues: 48.0308 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 924 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.219775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.181922 restraints weight = 7364.850| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.70 r_work: 0.4218 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7262 Z= 0.147 Angle : 0.653 11.976 10079 Z= 0.335 Chirality : 0.044 0.215 1186 Planarity : 0.005 0.059 1085 Dihedral : 17.124 79.957 1564 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 6.01 % Allowed : 29.88 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.65 (0.30), residues: 730 helix: 0.33 (0.35), residues: 229 sheet: -1.75 (0.37), residues: 146 loop : -1.74 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 570 TYR 0.016 0.002 TYR A 321 PHE 0.011 0.001 PHE A 758 TRP 0.024 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 7262) covalent geometry : angle 0.65293 / 0.34 (10079) hydrogen bonds : bond 0.04524 / 3.03 ( 312) hydrogen bonds : angle 5.34643 / 3.79 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6386 (ttm) REVERT: A 276 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6990 (mt) REVERT: A 329 MET cc_start: 0.7375 (tpp) cc_final: 0.7145 (mpp) REVERT: A 623 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6092 (mt) REVERT: A 647 ILE cc_start: 0.3835 (OUTLIER) cc_final: 0.2131 (pt) REVERT: A 671 ILE cc_start: 0.4009 (OUTLIER) cc_final: 0.3292 (tp) REVERT: A 672 MET cc_start: 0.5536 (mmp) cc_final: 0.5309 (mmt) REVERT: A 684 LYS cc_start: 0.6153 (tppt) cc_final: 0.5761 (mptt) REVERT: A 924 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7085 (mmtt) outliers start: 40 outliers final: 21 residues processed: 113 average time/residue: 0.4119 time to fit residues: 49.9162 Evaluate side-chains 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 924 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.213202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174937 restraints weight = 7390.043| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.69 r_work: 0.4151 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7262 Z= 0.247 Angle : 0.766 12.548 10079 Z= 0.390 Chirality : 0.050 0.216 1186 Planarity : 0.006 0.062 1085 Dihedral : 17.258 76.976 1564 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 7.66 % Allowed : 28.53 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.70 (0.29), residues: 730 helix: 0.17 (0.35), residues: 229 sheet: -1.43 (0.40), residues: 128 loop : -1.87 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.020 0.003 TYR A 321 PHE 0.014 0.002 PHE A 272 TRP 0.026 0.003 TRP A 358 HIS 0.007 0.002 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 ( 7262) covalent geometry : angle 0.76616 / 0.39 (10079) hydrogen bonds : bond 0.05851 / 3.96 ( 312) hydrogen bonds : angle 5.60504 / 3.92 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 81 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7126 (mt) REVERT: A 354 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.6090 (pmt-80) REVERT: A 647 ILE cc_start: 0.3384 (OUTLIER) cc_final: 0.1501 (pt) REVERT: A 671 ILE cc_start: 0.4444 (OUTLIER) cc_final: 0.3786 (tp) REVERT: A 697 ILE cc_start: 0.5178 (mm) cc_final: 0.4822 (mp) REVERT: A 918 MET cc_start: 0.5891 (ptp) cc_final: 0.5581 (ptm) outliers start: 51 outliers final: 29 residues processed: 118 average time/residue: 0.3794 time to fit residues: 47.7925 Evaluate side-chains 113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 954 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.216987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179140 restraints weight = 7323.744| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.69 r_work: 0.4186 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7262 Z= 0.159 Angle : 0.664 12.034 10079 Z= 0.343 Chirality : 0.045 0.232 1186 Planarity : 0.005 0.055 1085 Dihedral : 17.139 78.913 1564 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 5.56 % Allowed : 31.08 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.63 (0.30), residues: 730 helix: 0.26 (0.35), residues: 229 sheet: -1.68 (0.40), residues: 134 loop : -1.72 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.024 0.002 TYR A 321 PHE 0.011 0.001 PHE A 848 TRP 0.026 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 7262) covalent geometry : angle 0.66397 / 0.34 (10079) hydrogen bonds : bond 0.04631 / 3.14 ( 312) hydrogen bonds : angle 5.47242 / 3.86 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7038 (mt) REVERT: A 329 MET cc_start: 0.7488 (tpp) cc_final: 0.6956 (mpp) REVERT: A 354 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5492 (pmt-80) REVERT: A 671 ILE cc_start: 0.4477 (OUTLIER) cc_final: 0.3599 (tp) REVERT: A 918 MET cc_start: 0.5717 (ptp) cc_final: 0.5373 (ptm) outliers start: 37 outliers final: 26 residues processed: 111 average time/residue: 0.3296 time to fit residues: 39.3864 Evaluate side-chains 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.220515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.183179 restraints weight = 7447.793| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 1.61 r_work: 0.4235 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7262 Z= 0.191 Angle : 0.717 11.909 10079 Z= 0.365 Chirality : 0.048 0.317 1186 Planarity : 0.005 0.057 1085 Dihedral : 17.158 78.322 1564 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 5.86 % Allowed : 31.23 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.66 (0.30), residues: 730 helix: 0.25 (0.35), residues: 229 sheet: -1.67 (0.39), residues: 137 loop : -1.76 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 354 TYR 0.031 0.002 TYR A 321 PHE 0.011 0.002 PHE A 272 TRP 0.024 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 7262) covalent geometry : angle 0.71708 / 0.37 (10079) hydrogen bonds : bond 0.05044 / 3.44 ( 312) hydrogen bonds : angle 5.46731 / 3.84 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7206 (mt) REVERT: A 329 MET cc_start: 0.7580 (tpp) cc_final: 0.7026 (mpp) REVERT: A 354 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5753 (pmt-80) REVERT: A 678 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5851 (tm) REVERT: A 918 MET cc_start: 0.5852 (ptp) cc_final: 0.5569 (ptm) outliers start: 39 outliers final: 27 residues processed: 107 average time/residue: 0.3349 time to fit residues: 38.4858 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.221835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.184845 restraints weight = 7453.864| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 1.62 r_work: 0.4249 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7262 Z= 0.170 Angle : 0.707 11.878 10079 Z= 0.358 Chirality : 0.048 0.370 1186 Planarity : 0.005 0.056 1085 Dihedral : 17.089 79.006 1564 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 5.11 % Allowed : 31.68 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.62 (0.30), residues: 730 helix: 0.29 (0.34), residues: 229 sheet: -1.62 (0.38), residues: 147 loop : -1.74 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.037 0.002 TYR A 321 PHE 0.011 0.002 PHE A 758 TRP 0.023 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7262) covalent geometry : angle 0.70668 / 0.36 (10079) hydrogen bonds : bond 0.04648 / 3.17 ( 312) hydrogen bonds : angle 5.45023 / 3.85 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7218 (mt) REVERT: A 329 MET cc_start: 0.7546 (tpp) cc_final: 0.6999 (mpp) REVERT: A 354 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5870 (pmt-80) REVERT: A 678 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6034 (tm) REVERT: A 918 MET cc_start: 0.5795 (ptp) cc_final: 0.5538 (ptm) outliers start: 34 outliers final: 26 residues processed: 104 average time/residue: 0.3244 time to fit residues: 36.0592 Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.222260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.186055 restraints weight = 7386.942| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.59 r_work: 0.4258 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7262 Z= 0.158 Angle : 0.704 12.170 10079 Z= 0.353 Chirality : 0.048 0.332 1186 Planarity : 0.005 0.053 1085 Dihedral : 17.050 79.573 1564 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 4.95 % Allowed : 32.43 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.57 (0.30), residues: 730 helix: 0.34 (0.35), residues: 229 sheet: -1.62 (0.40), residues: 137 loop : -1.71 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.042 0.002 TYR A 321 PHE 0.012 0.002 PHE A 758 TRP 0.022 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 7262) covalent geometry : angle 0.70416 / 0.35 (10079) hydrogen bonds : bond 0.04579 / 3.15 ( 312) hydrogen bonds : angle 5.43799 / 3.83 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 329 MET cc_start: 0.7540 (tpp) cc_final: 0.6991 (mpp) REVERT: A 354 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5811 (pmt-80) REVERT: A 678 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.5981 (tm) outliers start: 33 outliers final: 26 residues processed: 103 average time/residue: 0.3939 time to fit residues: 43.2936 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.219545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.182566 restraints weight = 7368.474| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.61 r_work: 0.4225 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4140 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7262 Z= 0.206 Angle : 0.745 11.919 10079 Z= 0.375 Chirality : 0.050 0.322 1186 Planarity : 0.005 0.058 1085 Dihedral : 17.061 78.064 1564 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.86 % Favored : 90.00 % Rotamer: Outliers : 4.80 % Allowed : 32.28 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.64 (0.30), residues: 730 helix: 0.28 (0.35), residues: 229 sheet: -1.57 (0.39), residues: 147 loop : -1.78 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.046 0.002 TYR A 321 PHE 0.012 0.002 PHE A 272 TRP 0.023 0.002 TRP A 358 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 ( 7262) covalent geometry : angle 0.74535 / 0.38 (10079) hydrogen bonds : bond 0.05222 / 3.58 ( 312) hydrogen bonds : angle 5.51926 / 3.88 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.24 seconds wall clock time: 42 minutes 52.04 seconds (2572.04 seconds total)