Starting phenix.real_space_refine on Tue Aug 4 18:35:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.map" model { file = "/net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s1e_54446/08_2026/9s1e_54446.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 P 5 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 3689 2.51 5 N 1008 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 5806 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "B" Number of atoms: 5702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5702 Classifications: {'peptide': 717} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 684} Chain breaks: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 5, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.75, per 1000 atoms: 0.30 Number of scatterers: 5806 At special positions: 0 Unit cell: (75.8352, 79.9344, 116.827, 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) S 31 16.00 P 5 15.00 Mg 1 11.99 O 1072 8.00 N 1008 7.00 C 3689 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: 0.53 Conformation dependent library (CDL) restraints added in 308.2 milliseconds 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 34.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.659A pdb=" N GLN B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.719A pdb=" N GLU B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 305' Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.875A pdb=" N MET B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.102A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 Processing helix chain 'B' and resid 505 through 524 Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 538 through 550 Processing helix chain 'B' and resid 565 through 579 removed outlier: 3.682A pdb=" N TYR B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 593 removed outlier: 3.528A pdb=" N GLY B 593 " --> pdb=" O ARG B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 590 through 593' Processing helix chain 'B' and resid 594 through 614 removed outlier: 4.371A pdb=" N MET B 599 " --> pdb=" O GLN B 595 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA B 600 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 691 Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.602A pdb=" N VAL B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 726 Processing helix chain 'B' and resid 805 through 816 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 852 through 858 removed outlier: 4.032A pdb=" N ASN B 857 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 659 through 664 removed outlier: 4.964A pdb=" N ILE B 629 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 736 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 800 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 738 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 114 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 752 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 756 " --> pdb=" O SER B 753 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 257 through 259 removed outlier: 5.185A pdb=" N ILE B 264 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 164 removed outlier: 5.619A pdb=" N LEU B 130 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU B 201 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN B 132 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.749A pdb=" N ILE B 463 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 531 through 535 removed outlier: 6.591A pdb=" N LEU B 498 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU B 560 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 500 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 557 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 587 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N CYS B 559 " --> pdb=" O VAL B 587 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1867 1.34 - 1.46: 977 1.46 - 1.57: 3040 1.57 - 1.69: 9 1.69 - 1.81: 46 Bond restraints: 5939 Sorted by residual: bond pdb=" P C C 5 " pdb=" OP2 C C 5 " ideal model delta sigma weight residual 1.485 1.515 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" P C C 5 " pdb=" OP1 C C 5 " ideal model delta sigma weight residual 1.485 1.514 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" P C C 4 " pdb=" OP2 C C 4 " ideal model delta sigma weight residual 1.485 1.513 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" P U C 2 " pdb=" OP2 U C 2 " ideal model delta sigma weight residual 1.485 1.512 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 5934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 7894 1.56 - 3.12: 150 3.12 - 4.68: 26 4.68 - 6.24: 8 6.24 - 7.79: 7 Bond angle restraints: 8085 Sorted by residual: angle pdb=" CA GLU B 354 " pdb=" CB GLU B 354 " pdb=" CG GLU B 354 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" O5' C C 4 " pdb=" C5' C C 4 " pdb=" C4' C C 4 " ideal model delta sigma weight residual 109.40 112.04 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" CA GLU B 692 " pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.46e+00 angle pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " pdb=" CD GLU B 692 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.70e+00 3.46e-01 8.69e+00 angle pdb=" CG ARG B 504 " pdb=" CD ARG B 504 " pdb=" NE ARG B 504 " ideal model delta sigma weight residual 112.00 118.34 -6.34 2.20e+00 2.07e-01 8.30e+00 ... (remaining 8080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3050 17.75 - 35.50: 364 35.50 - 53.24: 119 53.24 - 70.99: 38 70.99 - 88.74: 7 Dihedral angle restraints: 3578 sinusoidal: 1473 harmonic: 2105 Sorted by residual: dihedral pdb=" CA ASP B 357 " pdb=" CB ASP B 357 " pdb=" CG ASP B 357 " pdb=" OD1 ASP B 357 " ideal model delta sinusoidal sigma weight residual -30.00 -86.41 56.41 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 800 " pdb=" CB ASP B 800 " pdb=" CG ASP B 800 " pdb=" OD1 ASP B 800 " ideal model delta sinusoidal sigma weight residual -30.00 -85.67 55.67 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU B 201 " pdb=" CG GLU B 201 " pdb=" CD GLU B 201 " pdb=" OE1 GLU B 201 " ideal model delta sinusoidal sigma weight residual 0.00 -88.74 88.74 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 714 0.048 - 0.096: 143 0.096 - 0.144: 65 0.144 - 0.192: 1 0.192 - 0.240: 1 Chirality restraints: 924 Sorted by residual: chirality pdb=" P U C 1 " pdb=" OP1 U C 1 " pdb=" OP2 U C 1 " pdb=" O5' U C 1 " both_signs ideal model delta sigma weight residual True 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR B 520 " pdb=" N THR B 520 " pdb=" C THR B 520 " pdb=" CB THR B 520 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL B 829 " pdb=" N VAL B 829 " pdb=" C VAL B 829 " pdb=" CB VAL B 829 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 921 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 829 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO B 830 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 830 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 830 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 622 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 623 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 582 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 583 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.022 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 37 2.51 - 3.11: 4067 3.11 - 3.71: 8929 3.71 - 4.30: 13064 4.30 - 4.90: 21959 Nonbonded interactions: 48056 Sorted by model distance: nonbonded pdb=" O LEU B 862 " pdb="MG MG B 901 " model vdw 1.914 2.170 nonbonded pdb=" OP3 U C 1 " pdb="MG MG B 901 " model vdw 2.074 2.170 nonbonded pdb=" OP1 A C 3 " pdb="MG MG B 901 " model vdw 2.110 2.170 nonbonded pdb=" OE1 GLN B 608 " pdb="MG MG B 901 " model vdw 2.123 2.170 nonbonded pdb=" OXT LEU B 862 " pdb="MG MG B 901 " model vdw 2.167 2.170 ... (remaining 48051 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: 3.330 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5939 Z= 0.184 Angle : 0.601 7.794 8085 Z= 0.305 Chirality : 0.046 0.240 924 Planarity : 0.004 0.065 1013 Dihedral : 18.083 88.738 2220 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.28 % Allowed : 33.07 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.30), residues: 709 helix: -0.32 (0.32), residues: 224 sheet: 0.08 (0.38), residues: 173 loop : -0.48 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 504 TYR 0.009 0.002 TYR B 776 PHE 0.011 0.002 PHE B 779 TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 5939) covalent geometry : angle 0.60104 / 0.31 ( 8085) hydrogen bonds : bond 0.23597 / 21.19 ( 255) hydrogen bonds : angle 7.94955 / 6.39 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.4495 time to fit residues: 32.0182 Evaluate side-chains 54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.0040 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 ASN B 691 ASN B 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096051 restraints weight = 10309.553| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.49 r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5939 Z= 0.135 Angle : 0.589 9.384 8085 Z= 0.304 Chirality : 0.045 0.164 924 Planarity : 0.005 0.074 1013 Dihedral : 8.314 73.302 875 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.82 % Allowed : 28.57 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.31), residues: 709 helix: 1.19 (0.35), residues: 222 sheet: -0.34 (0.38), residues: 174 loop : -0.33 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.010 0.001 TYR B 776 PHE 0.017 0.002 PHE B 648 TRP 0.007 0.001 TRP B 479 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 5939) covalent geometry : angle 0.58947 / 0.30 ( 8085) hydrogen bonds : bond 0.04964 / 4.48 ( 255) hydrogen bonds : angle 5.50233 / 4.55 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 314 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8782 (p0) REVERT: B 470 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5538 (p90) outliers start: 30 outliers final: 14 residues processed: 75 average time/residue: 0.3719 time to fit residues: 29.6534 Evaluate side-chains 60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 741 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 ASN B 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096418 restraints weight = 10197.672| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.46 r_work: 0.3214 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.003 0.037 5939 Z= 0.134 Angle : 0.558 12.671 8085 Z= 0.283 Chirality : 0.044 0.156 924 Planarity : 0.004 0.075 1013 Dihedral : 8.033 73.434 870 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.14 % Allowed : 27.45 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.31), residues: 709 helix: 1.31 (0.35), residues: 223 sheet: -0.50 (0.37), residues: 182 loop : -0.25 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 503 TYR 0.012 0.001 TYR B 776 PHE 0.016 0.001 PHE B 648 TRP 0.007 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5939) covalent geometry : angle 0.55776 / 0.28 ( 8085) hydrogen bonds : bond 0.04141 / 3.74 ( 255) hydrogen bonds : angle 5.08335 / 4.26 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: B 354 GLU cc_start: 0.5784 (tm-30) cc_final: 0.5511 (tm-30) REVERT: B 355 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5572 (tp) REVERT: B 421 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: B 470 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5465 (p90) outliers start: 32 outliers final: 15 residues processed: 73 average time/residue: 0.3618 time to fit residues: 28.0501 Evaluate side-chains 64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 741 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 ASN B 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095625 restraints weight = 10380.760| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.48 r_work: 0.3191 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5939 Z= 0.168 Angle : 0.569 10.153 8085 Z= 0.284 Chirality : 0.045 0.153 924 Planarity : 0.004 0.078 1013 Dihedral : 8.037 73.410 870 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.30 % Allowed : 28.09 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.31), residues: 709 helix: 1.32 (0.35), residues: 223 sheet: -0.68 (0.35), residues: 193 loop : -0.21 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.011 0.001 TYR B 776 PHE 0.024 0.002 PHE B 283 TRP 0.007 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 5939) covalent geometry : angle 0.56859 / 0.28 ( 8085) hydrogen bonds : bond 0.03830 / 3.46 ( 255) hydrogen bonds : angle 4.92336 / 4.13 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8388 (m-30) REVERT: B 298 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: B 354 GLU cc_start: 0.6065 (tm-30) cc_final: 0.5850 (tm-30) REVERT: B 355 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5511 (tp) REVERT: B 470 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5608 (p90) REVERT: B 528 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7951 (tttp) outliers start: 33 outliers final: 16 residues processed: 75 average time/residue: 0.3668 time to fit residues: 29.2882 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 741 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 505 ASN B 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096541 restraints weight = 10359.599| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.51 r_work: 0.3205 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5939 Z= 0.125 Angle : 0.535 8.264 8085 Z= 0.268 Chirality : 0.044 0.153 924 Planarity : 0.004 0.076 1013 Dihedral : 7.932 73.400 870 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.82 % Allowed : 28.09 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.31), residues: 709 helix: 1.45 (0.35), residues: 223 sheet: -0.75 (0.36), residues: 185 loop : -0.21 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 319 TYR 0.013 0.001 TYR B 776 PHE 0.015 0.001 PHE B 648 TRP 0.007 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5939) covalent geometry : angle 0.53452 / 0.27 ( 8085) hydrogen bonds : bond 0.03455 / 3.09 ( 255) hydrogen bonds : angle 4.72950 / 3.98 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7392 (mmm160) REVERT: B 241 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: B 298 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: B 355 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5271 (tp) REVERT: B 428 TYR cc_start: 0.7165 (t80) cc_final: 0.6951 (t80) REVERT: B 470 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5489 (p90) outliers start: 30 outliers final: 18 residues processed: 76 average time/residue: 0.4234 time to fit residues: 34.0001 Evaluate side-chains 69 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096588 restraints weight = 10358.407| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.48 r_work: 0.3188 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5939 Z= 0.173 Angle : 0.570 8.392 8085 Z= 0.283 Chirality : 0.045 0.151 924 Planarity : 0.004 0.077 1013 Dihedral : 7.961 73.391 870 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.46 % Allowed : 27.61 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.31), residues: 709 helix: 1.37 (0.35), residues: 223 sheet: -0.78 (0.36), residues: 185 loop : -0.20 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 748 TYR 0.011 0.001 TYR B 776 PHE 0.023 0.002 PHE B 283 TRP 0.008 0.001 TRP B 479 HIS 0.003 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 5939) covalent geometry : angle 0.56970 / 0.28 ( 8085) hydrogen bonds : bond 0.03602 / 3.23 ( 255) hydrogen bonds : angle 4.76656 / 3.99 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7423 (mmm160) REVERT: B 241 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: B 284 MET cc_start: 0.8188 (ptt) cc_final: 0.7967 (ptp) REVERT: B 298 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: B 470 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5535 (p90) REVERT: B 528 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8005 (tttm) outliers start: 34 outliers final: 20 residues processed: 77 average time/residue: 0.4028 time to fit residues: 32.7951 Evaluate side-chains 70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095326 restraints weight = 10432.739| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.50 r_work: 0.3184 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5939 Z= 0.177 Angle : 0.595 12.276 8085 Z= 0.293 Chirality : 0.045 0.152 924 Planarity : 0.004 0.076 1013 Dihedral : 7.972 73.369 870 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.49 % Allowed : 29.05 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.31), residues: 709 helix: 1.37 (0.34), residues: 223 sheet: -0.75 (0.37), residues: 182 loop : -0.18 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 756 TYR 0.012 0.001 TYR B 776 PHE 0.014 0.002 PHE B 648 TRP 0.008 0.001 TRP B 479 HIS 0.003 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 5939) covalent geometry : angle 0.59536 / 0.29 ( 8085) hydrogen bonds : bond 0.03590 / 3.23 ( 255) hydrogen bonds : angle 4.76032 / 3.98 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8422 (m-30) REVERT: B 284 MET cc_start: 0.8202 (ptt) cc_final: 0.7959 (ptp) REVERT: B 298 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: B 470 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5559 (p90) REVERT: B 528 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8029 (tttm) outliers start: 28 outliers final: 20 residues processed: 71 average time/residue: 0.4019 time to fit residues: 30.1965 Evaluate side-chains 69 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095968 restraints weight = 10371.808| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.51 r_work: 0.3198 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5939 Z= 0.135 Angle : 0.581 13.106 8085 Z= 0.283 Chirality : 0.044 0.151 924 Planarity : 0.004 0.076 1013 Dihedral : 7.892 73.382 870 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.53 % Allowed : 30.66 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.31), residues: 709 helix: 1.52 (0.35), residues: 223 sheet: -0.71 (0.37), residues: 181 loop : -0.21 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.013 0.001 TYR B 776 PHE 0.029 0.002 PHE B 283 TRP 0.007 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 5939) covalent geometry : angle 0.58087 / 0.28 ( 8085) hydrogen bonds : bond 0.03334 / 2.99 ( 255) hydrogen bonds : angle 4.63185 / 3.89 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (m-30) REVERT: B 284 MET cc_start: 0.8182 (ptt) cc_final: 0.7951 (ptp) REVERT: B 298 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 428 TYR cc_start: 0.7162 (t80) cc_final: 0.6939 (t80) REVERT: B 470 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5543 (p90) outliers start: 22 outliers final: 17 residues processed: 68 average time/residue: 0.3622 time to fit residues: 26.1414 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.0010 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095818 restraints weight = 10385.806| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.51 r_work: 0.3209 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5939 Z= 0.139 Angle : 0.597 12.838 8085 Z= 0.295 Chirality : 0.045 0.151 924 Planarity : 0.004 0.076 1013 Dihedral : 7.869 73.389 869 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.17 % Allowed : 29.70 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.31), residues: 709 helix: 1.66 (0.35), residues: 217 sheet: -0.80 (0.36), residues: 183 loop : -0.14 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 174 TYR 0.013 0.001 TYR B 776 PHE 0.022 0.002 PHE B 401 TRP 0.007 0.001 TRP B 479 HIS 0.003 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5939) covalent geometry : angle 0.59694 / 0.29 ( 8085) hydrogen bonds : bond 0.03336 / 3.01 ( 255) hydrogen bonds : angle 4.59455 / 3.86 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: B 284 MET cc_start: 0.8192 (ptt) cc_final: 0.7941 (ptp) REVERT: B 298 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: B 401 PHE cc_start: 0.8385 (t80) cc_final: 0.7797 (t80) REVERT: B 405 LYS cc_start: 0.8582 (pttm) cc_final: 0.8285 (mtmt) REVERT: B 421 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 528 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8062 (tttm) outliers start: 26 outliers final: 18 residues processed: 69 average time/residue: 0.3873 time to fit residues: 28.3669 Evaluate side-chains 68 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095274 restraints weight = 10462.863| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.52 r_work: 0.3190 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5939 Z= 0.168 Angle : 0.617 14.820 8085 Z= 0.301 Chirality : 0.045 0.150 924 Planarity : 0.004 0.076 1013 Dihedral : 7.922 73.356 869 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.33 % Allowed : 29.70 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.31), residues: 709 helix: 1.56 (0.35), residues: 217 sheet: -0.80 (0.36), residues: 180 loop : -0.16 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 748 TYR 0.011 0.001 TYR B 776 PHE 0.027 0.002 PHE B 283 TRP 0.010 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 5939) covalent geometry : angle 0.61664 / 0.30 ( 8085) hydrogen bonds : bond 0.03440 / 3.10 ( 255) hydrogen bonds : angle 4.66967 / 3.91 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: B 284 MET cc_start: 0.8197 (ptt) cc_final: 0.7958 (ptp) REVERT: B 298 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 401 PHE cc_start: 0.8500 (t80) cc_final: 0.7926 (t80) REVERT: B 405 LYS cc_start: 0.8590 (pttm) cc_final: 0.8271 (mtmt) REVERT: B 421 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 428 TYR cc_start: 0.7235 (t80) cc_final: 0.7012 (t80) REVERT: B 528 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8039 (tttm) outliers start: 27 outliers final: 16 residues processed: 70 average time/residue: 0.3656 time to fit residues: 27.1153 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 838 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.123333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096866 restraints weight = 10210.758| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.50 r_work: 0.3227 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5939 Z= 0.115 Angle : 0.588 15.114 8085 Z= 0.285 Chirality : 0.044 0.164 924 Planarity : 0.004 0.074 1013 Dihedral : 7.798 73.380 867 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.05 % Allowed : 30.50 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.32), residues: 709 helix: 1.77 (0.35), residues: 217 sheet: -0.78 (0.37), residues: 180 loop : -0.20 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 437 TYR 0.014 0.001 TYR B 776 PHE 0.021 0.001 PHE B 401 TRP 0.006 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 5939) covalent geometry : angle 0.58816 / 0.29 ( 8085) hydrogen bonds : bond 0.03125 / 2.79 ( 255) hydrogen bonds : angle 4.51133 / 3.78 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1682.37 seconds wall clock time: 29 minutes 24.37 seconds (1764.37 seconds total)