Starting phenix.real_space_refine on Tue Mar 11 22:40:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij3_60614/03_2025/9ij3_60614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij3_60614/03_2025/9ij3_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_60614/03_2025/9ij3_60614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij3_60614/03_2025/9ij3_60614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij3_60614/03_2025/9ij3_60614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij3_60614/03_2025/9ij3_60614.cif" } resolution = 2.6 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 4.54, per 1000 atoms: 0.65 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: 2.10 Conformation dependent library (CDL) restraints added in 715.6 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: 2.66 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: 3.57 Time building geometry restraints manager: 2.27 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: 9954 3.40 - 6.80: 101 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=" 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 angle pdb=" N ILE A 879 " pdb=" CA ILE A 879 " pdb=" C ILE A 879 " ideal model delta sigma weight residual 113.20 107.86 5.34 9.60e-01 1.09e+00 3.09e+01 angle pdb=" C4' C B 8 " pdb=" C3' C B 8 " pdb=" O3' C B 8 " ideal model delta sigma weight residual 113.00 104.82 8.18 1.50e+00 4.44e-01 2.97e+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: 1016 0.077 - 0.154: 159 0.154 - 0.230: 9 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: 0.280 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.230 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 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= 0.301 Angle : 0.987 17.007 10079 Z= 0.512 Chirality : 0.053 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 (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: -2.04 (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 TRP 0.070 0.003 TRP A 358 HIS 0.009 0.001 HIS A 472 PHE 0.016 0.002 PHE A 758 TYR 0.031 0.003 TYR A 425 ARG 0.004 0.000 ARG A 570 *********************** 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 : 0.694 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: 1.0165 time to fit residues: 111.6238 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 : 0.653 ------------------------------------------------------------------------------- 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 65 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 954 GLN A 958 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.225753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.189219 restraints weight = 7280.364| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 1.58 r_work: 0.4295 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7262 Z= 0.293 Angle : 0.728 12.167 10079 Z= 0.367 Chirality : 0.047 0.283 1186 Planarity : 0.006 0.069 1085 Dihedral : 17.422 81.962 1568 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.49 % Favored : 91.37 % Rotamer: Outliers : 6.46 % Allowed : 28.83 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.72 (0.30), residues: 730 helix: -0.06 (0.34), residues: 233 sheet: -1.41 (0.40), residues: 140 loop : -1.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 358 HIS 0.008 0.001 HIS A 472 PHE 0.014 0.002 PHE A 325 TYR 0.012 0.002 TYR A 241 ARG 0.005 0.001 ARG A 937 *********************** 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 131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5853 (mp) REVERT: A 228 LEU cc_start: 0.3056 (OUTLIER) cc_final: 0.2364 (mt) REVERT: A 276 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 329 MET cc_start: 0.7498 (tpp) cc_final: 0.7169 (mpp) REVERT: A 429 ASP cc_start: 0.5911 (t0) cc_final: 0.5675 (t0) REVERT: A 519 ILE cc_start: 0.6534 (mt) cc_final: 0.6070 (mt) REVERT: A 623 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6157 (mt) REVERT: A 831 LEU cc_start: 0.6344 (tp) cc_final: 0.6111 (tp) outliers start: 43 outliers final: 17 residues processed: 110 average time/residue: 0.9103 time to fit residues: 107.5221 Evaluate side-chains 108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 254 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 623 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** 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 = 0.4582 r_free = 0.4582 target = 0.214820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.176500 restraints weight = 7359.865| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 1.69 r_work: 0.4163 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7262 Z= 0.345 Angle : 0.751 11.028 10079 Z= 0.380 Chirality : 0.048 0.255 1186 Planarity : 0.006 0.063 1085 Dihedral : 17.388 80.108 1564 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.68 % Rotamer: Outliers : 6.16 % Allowed : 28.38 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.73 (0.30), residues: 730 helix: 0.02 (0.34), residues: 231 sheet: -1.68 (0.39), residues: 138 loop : -1.68 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 358 HIS 0.009 0.002 HIS A 472 PHE 0.013 0.002 PHE A 758 TYR 0.011 0.002 TYR A 420 ARG 0.005 0.001 ARG A 937 *********************** 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 127 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3491 (OUTLIER) cc_final: 0.2913 (mt) REVERT: A 276 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 623 LEU cc_start: 0.6470 (mm) cc_final: 0.6212 (mt) REVERT: A 671 ILE cc_start: 0.4083 (OUTLIER) cc_final: 0.3351 (tp) REVERT: A 672 MET cc_start: 0.5499 (mmp) cc_final: 0.5022 (mmm) REVERT: A 918 MET cc_start: 0.5867 (ptp) cc_final: 0.5597 (ptm) outliers start: 41 outliers final: 19 residues processed: 114 average time/residue: 0.8293 time to fit residues: 102.2889 Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 VAL 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 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 ILE 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 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 898 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 958 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.215047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.177589 restraints weight = 7498.636| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.61 r_work: 0.4179 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4088 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 7262 Z= 0.447 Angle : 0.824 10.822 10079 Z= 0.416 Chirality : 0.051 0.281 1186 Planarity : 0.006 0.071 1085 Dihedral : 17.523 75.888 1564 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 7.66 % Allowed : 27.03 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.87 (0.30), residues: 730 helix: -0.10 (0.34), residues: 228 sheet: -1.66 (0.39), residues: 135 loop : -1.80 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 358 HIS 0.009 0.002 HIS A 472 PHE 0.014 0.002 PHE A 272 TYR 0.014 0.003 TYR A 888 ARG 0.007 0.001 ARG A 937 *********************** 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 139 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3569 (OUTLIER) cc_final: 0.3034 (mt) REVERT: A 276 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7268 (mt) REVERT: A 329 MET cc_start: 0.7464 (tpp) cc_final: 0.7204 (mpp) REVERT: A 623 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6464 (mt) REVERT: A 671 ILE cc_start: 0.4633 (OUTLIER) cc_final: 0.4019 (tp) outliers start: 51 outliers final: 28 residues processed: 124 average time/residue: 0.8655 time to fit residues: 115.6662 Evaluate side-chains 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 ASN 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 461 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU 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 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 905 ILE Chi-restraints excluded: chain A residue 954 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4695 r_free = 0.4695 target = 0.222766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.186021 restraints weight = 7349.808| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 1.60 r_work: 0.4259 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7262 Z= 0.217 Angle : 0.653 10.349 10079 Z= 0.332 Chirality : 0.045 0.226 1186 Planarity : 0.005 0.057 1085 Dihedral : 17.257 82.111 1564 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 4.80 % Allowed : 31.83 % 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 (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: -1.66 (0.30), residues: 730 helix: 0.20 (0.34), residues: 229 sheet: -1.69 (0.40), residues: 133 loop : -1.70 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 PHE 0.012 0.001 PHE A 950 TYR 0.017 0.002 TYR A 321 ARG 0.006 0.000 ARG A 570 *********************** 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 120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6760 (mp0) cc_final: 0.6532 (mp0) REVERT: A 276 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7222 (mt) REVERT: A 329 MET cc_start: 0.7411 (tpp) cc_final: 0.7117 (mpp) REVERT: A 623 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6211 (mt) REVERT: A 671 ILE cc_start: 0.4295 (OUTLIER) cc_final: 0.3510 (tp) REVERT: A 684 LYS cc_start: 0.6051 (tppt) cc_final: 0.5817 (mptt) REVERT: A 726 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6839 (mt-10) outliers start: 32 outliers final: 12 residues processed: 106 average time/residue: 0.9564 time to fit residues: 108.6733 Evaluate side-chains 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 505 MET 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 726 GLU 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 868 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 64 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4689 r_free = 0.4689 target = 0.221903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.185791 restraints weight = 7383.695| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 1.58 r_work: 0.4258 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4169 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7262 Z= 0.232 Angle : 0.672 13.061 10079 Z= 0.336 Chirality : 0.045 0.227 1186 Planarity : 0.005 0.053 1085 Dihedral : 17.165 82.076 1564 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 4.80 % Allowed : 31.98 % 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 (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: -1.61 (0.30), residues: 730 helix: 0.31 (0.34), residues: 229 sheet: -1.77 (0.39), residues: 137 loop : -1.68 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.001 PHE A 758 TYR 0.025 0.002 TYR A 321 ARG 0.004 0.000 ARG A 354 *********************** 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 118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7217 (mt) REVERT: A 671 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.3645 (tp) REVERT: A 726 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: A 753 ARG cc_start: 0.5984 (tpt170) cc_final: 0.5764 (tpt170) outliers start: 32 outliers final: 16 residues processed: 107 average time/residue: 0.8685 time to fit residues: 99.9048 Evaluate side-chains 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 505 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 755 VAL 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 898 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4601 r_free = 0.4601 target = 0.223350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.184140 restraints weight = 6784.814| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.73 r_work: 0.4124 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7262 Z= 0.198 Angle : 0.633 12.120 10079 Z= 0.318 Chirality : 0.044 0.205 1186 Planarity : 0.005 0.054 1085 Dihedral : 17.046 83.661 1564 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % 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 (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: -1.46 (0.30), residues: 730 helix: 0.46 (0.34), residues: 229 sheet: -1.51 (0.38), residues: 141 loop : -1.67 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 358 HIS 0.004 0.001 HIS A 472 PHE 0.013 0.001 PHE A 758 TYR 0.030 0.002 TYR A 321 ARG 0.004 0.000 ARG A 570 *********************** 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: 32 poor density : 90 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6538 (mp0) cc_final: 0.6269 (mp0) REVERT: A 276 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6885 (mt) REVERT: A 329 MET cc_start: 0.7126 (tpp) cc_final: 0.6874 (mpp) REVERT: A 671 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3578 (tp) outliers start: 32 outliers final: 16 residues processed: 111 average time/residue: 0.8947 time to fit residues: 106.6887 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL 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 917 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4595 r_free = 0.4595 target = 0.222753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183830 restraints weight = 6860.819| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.68 r_work: 0.4118 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7262 Z= 0.204 Angle : 0.631 10.218 10079 Z= 0.317 Chirality : 0.044 0.194 1186 Planarity : 0.005 0.046 1085 Dihedral : 16.962 83.074 1564 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 4.20 % Allowed : 33.78 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.40 (0.30), residues: 730 helix: 0.50 (0.34), residues: 229 sheet: -1.48 (0.38), residues: 143 loop : -1.63 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.001 PHE A 758 TYR 0.036 0.002 TYR A 321 ARG 0.003 0.000 ARG A 570 *********************** 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 113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6575 (mp0) cc_final: 0.6298 (mp0) REVERT: A 276 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6916 (mt) REVERT: A 329 MET cc_start: 0.7158 (tpp) cc_final: 0.6868 (mpp) REVERT: A 671 ILE cc_start: 0.4104 (OUTLIER) cc_final: 0.3354 (tp) REVERT: A 672 MET cc_start: 0.5542 (mmp) cc_final: 0.5117 (mmp) REVERT: A 753 ARG cc_start: 0.5684 (tpt170) cc_final: 0.5397 (tpt170) outliers start: 28 outliers final: 20 residues processed: 105 average time/residue: 0.9374 time to fit residues: 106.1377 Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 358 TRP Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL 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 898 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4597 r_free = 0.4597 target = 0.222894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183653 restraints weight = 6853.673| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.69 r_work: 0.4116 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7262 Z= 0.211 Angle : 0.630 8.069 10079 Z= 0.319 Chirality : 0.045 0.258 1186 Planarity : 0.005 0.047 1085 Dihedral : 16.914 82.877 1564 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.14 % Rotamer: Outliers : 3.60 % Allowed : 33.93 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.37 (0.30), residues: 730 helix: 0.53 (0.34), residues: 229 sheet: -1.45 (0.39), residues: 143 loop : -1.62 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.013 0.001 PHE A 758 TYR 0.041 0.002 TYR A 321 ARG 0.004 0.000 ARG A 570 *********************** 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 108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6687 (mp0) cc_final: 0.6428 (mp0) REVERT: A 276 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 329 MET cc_start: 0.7215 (tpp) cc_final: 0.6932 (mpp) REVERT: A 671 ILE cc_start: 0.4090 (OUTLIER) cc_final: 0.3345 (tp) REVERT: A 672 MET cc_start: 0.5597 (mmp) cc_final: 0.5135 (mmp) outliers start: 24 outliers final: 20 residues processed: 100 average time/residue: 0.8885 time to fit residues: 95.7028 Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL 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 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 46 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4561 r_free = 0.4561 target = 0.218695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178575 restraints weight = 6884.462| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.70 r_work: 0.4063 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7262 Z= 0.281 Angle : 0.682 8.580 10079 Z= 0.347 Chirality : 0.047 0.265 1186 Planarity : 0.005 0.053 1085 Dihedral : 16.988 80.327 1564 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.86 % Favored : 90.00 % Rotamer: Outliers : 3.75 % Allowed : 34.23 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.52 (0.30), residues: 730 helix: 0.37 (0.34), residues: 230 sheet: -1.67 (0.39), residues: 137 loop : -1.63 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 358 HIS 0.006 0.001 HIS A 472 PHE 0.012 0.002 PHE A 272 TYR 0.054 0.002 TYR A 321 ARG 0.003 0.000 ARG A 570 ********************** 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 105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.6545 (mp0) cc_final: 0.6332 (mp0) REVERT: A 276 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6891 (mt) REVERT: A 329 MET cc_start: 0.7248 (tpp) cc_final: 0.6920 (mpp) REVERT: A 671 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3415 (tp) REVERT: A 672 MET cc_start: 0.5541 (mmp) cc_final: 0.5077 (mmp) REVERT: A 918 MET cc_start: 0.5238 (ptp) cc_final: 0.4843 (ptm) outliers start: 25 outliers final: 19 residues processed: 97 average time/residue: 0.9491 time to fit residues: 98.8138 Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 505 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 755 VAL 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 898 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4551 r_free = 0.4551 target = 0.217601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.177471 restraints weight = 6820.321| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.69 r_work: 0.4057 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7262 Z= 0.300 Angle : 0.716 15.307 10079 Z= 0.360 Chirality : 0.048 0.263 1186 Planarity : 0.005 0.055 1085 Dihedral : 17.016 79.809 1564 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.27 % Favored : 89.59 % Rotamer: Outliers : 3.60 % Allowed : 33.93 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.56 (0.30), residues: 730 helix: 0.27 (0.34), residues: 230 sheet: -1.45 (0.40), residues: 131 loop : -1.74 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 358 HIS 0.007 0.001 HIS A 472 PHE 0.012 0.002 PHE A 272 TYR 0.058 0.003 TYR A 321 ARG 0.003 0.001 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5453.56 seconds wall clock time: 93 minutes 49.94 seconds (5629.94 seconds total)