Starting phenix.real_space_refine on Thu Jul 2 02:45:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s1e_54446/07_2026/9s1e_54446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s1e_54446/07_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_54446/07_2026/9s1e_54446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s1e_54446/07_2026/9s1e_54446.map" model { file = "/net/cci-nas-00/data/ceres_data/9s1e_54446/07_2026/9s1e_54446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s1e_54446/07_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-dev-6108/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: 1.27, per 1000 atoms: 0.22 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: 0.45 Conformation dependent library (CDL) restraints added in 318.9 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: 0.13 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: 0.81 Time building geometry restraints manager: 0.60 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: 7906 1.56 - 3.12: 138 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=" 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 angle pdb=" C GLU B 354 " pdb=" CA GLU B 354 " pdb=" CB GLU B 354 " ideal model delta sigma weight residual 109.72 113.38 -3.66 1.61e+00 3.86e-01 5.17e+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: 720 0.048 - 0.096: 141 0.096 - 0.144: 61 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: 2.570 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: 6.050 Find NCS groups from input model: 0.100 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:5.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- 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= 0.183 Angle : 0.593 7.794 8085 Z= 0.296 Chirality : 0.045 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 0.59326 / 0.30 ( 8085) hydrogen bonds : bond 0.23597 / 20.48 ( 255) hydrogen bonds : angle 7.94955 / 6.22 ( 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 : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.4448 time to fit residues: 31.7239 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 : 0.188 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.122895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096090 restraints weight = 10301.415| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.48 r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5939 Z= 0.133 Angle : 0.586 9.438 8085 Z= 0.301 Chirality : 0.045 0.161 924 Planarity : 0.005 0.074 1013 Dihedral : 8.418 73.257 875 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.03 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: 0.13 (0.31), residues: 709 helix: 1.18 (0.35), residues: 222 sheet: -0.35 (0.38), residues: 174 loop : -0.33 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.010 0.001 TYR B 776 PHE 0.016 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 0.00301 / 0.13 ( 5939) covalent geometry : angle 0.58643 / 0.30 ( 8085) hydrogen bonds : bond 0.05045 / 4.37 ( 255) hydrogen bonds : angle 5.51597 / 4.46 ( 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 : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 314 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8778 (p0) REVERT: B 470 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5537 (p90) outliers start: 30 outliers final: 14 residues processed: 75 average time/residue: 0.3730 time to fit residues: 29.5829 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 : 0.143 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.0030 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 overall best weight: 0.2398 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.124038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097351 restraints weight = 10207.248| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.48 r_work: 0.3232 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1484 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= 0.111 Angle : 0.545 12.876 8085 Z= 0.276 Chirality : 0.044 0.158 924 Planarity : 0.004 0.074 1013 Dihedral : 8.093 73.439 870 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.17 % Allowed : 28.73 % 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: 0.19 (0.31), residues: 709 helix: 1.37 (0.35), residues: 223 sheet: -0.54 (0.37), residues: 185 loop : -0.24 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.012 0.001 TYR B 776 PHE 0.017 0.001 PHE B 648 TRP 0.006 0.001 TRP B 479 HIS 0.005 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5939) covalent geometry : angle 0.54481 / 0.28 ( 8085) hydrogen bonds : bond 0.04020 / 3.48 ( 255) hydrogen bonds : angle 5.06323 / 4.13 ( 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 74 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 GLU cc_start: 0.5735 (tm-30) cc_final: 0.5440 (tm-30) REVERT: B 355 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5569 (tp) REVERT: B 421 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: B 470 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5484 (p90) outliers start: 26 outliers final: 14 residues processed: 68 average time/residue: 0.4246 time to fit residues: 30.6559 Evaluate side-chains 61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 180 THR Chi-restraints excluded: chain B residue 198 LEU 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 407 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 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: 1.9990 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097189 restraints weight = 10319.642| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.50 r_work: 0.3219 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1690 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= 0.123 Angle : 0.536 10.573 8085 Z= 0.268 Chirality : 0.044 0.152 924 Planarity : 0.004 0.077 1013 Dihedral : 8.023 73.428 870 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.30 % Allowed : 27.77 % 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: 0.21 (0.31), residues: 709 helix: 1.45 (0.35), residues: 223 sheet: -0.59 (0.37), residues: 185 loop : -0.24 (0.35), residues: 301 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 0.023 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 0.00292 / 0.12 ( 5939) covalent geometry : angle 0.53595 / 0.27 ( 8085) hydrogen bonds : bond 0.03579 / 3.11 ( 255) hydrogen bonds : angle 4.79416 / 3.92 ( 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 : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: B 298 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: B 355 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5274 (tp) REVERT: B 421 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6874 (mp0) outliers start: 33 outliers final: 16 residues processed: 75 average time/residue: 0.3551 time to fit residues: 28.3171 Evaluate side-chains 65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 421 GLU 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 599 MET Chi-restraints excluded: chain B residue 622 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: 0.8980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.122577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096052 restraints weight = 10428.514| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.50 r_work: 0.3193 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: 0.7978 moved from start: 0.1720 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= 0.165 Angle : 0.553 7.817 8085 Z= 0.279 Chirality : 0.045 0.150 924 Planarity : 0.004 0.077 1013 Dihedral : 8.076 73.404 870 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 0.18 (0.31), residues: 709 helix: 1.40 (0.35), residues: 223 sheet: -0.61 (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 319 TYR 0.011 0.001 TYR B 776 PHE 0.015 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 0.00395 / 0.17 ( 5939) covalent geometry : angle 0.55317 / 0.28 ( 8085) hydrogen bonds : bond 0.03658 / 3.20 ( 255) hydrogen bonds : angle 4.77164 / 3.88 ( 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 80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: B 298 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 355 ILE cc_start: 0.5686 (OUTLIER) cc_final: 0.5417 (tp) REVERT: B 421 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 528 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7938 (tttp) outliers start: 30 outliers final: 17 residues processed: 78 average time/residue: 0.4398 time to fit residues: 36.3543 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 758 GLN 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: 1.9990 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.122582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096105 restraints weight = 10320.506| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.48 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5939 Z= 0.157 Angle : 0.549 7.302 8085 Z= 0.277 Chirality : 0.044 0.150 924 Planarity : 0.004 0.077 1013 Dihedral : 8.056 73.407 870 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 0.16 (0.31), residues: 709 helix: 1.41 (0.35), residues: 223 sheet: -0.66 (0.37), residues: 182 loop : -0.25 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 748 TYR 0.011 0.001 TYR B 776 PHE 0.024 0.002 PHE B 283 TRP 0.008 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 5939) covalent geometry : angle 0.54905 / 0.28 ( 8085) hydrogen bonds : bond 0.03535 / 3.08 ( 255) hydrogen bonds : angle 4.72620 / 3.84 ( 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 77 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7412 (mmm160) REVERT: B 241 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: B 298 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: B 355 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5635 (tp) REVERT: B 428 TYR cc_start: 0.7252 (t80) cc_final: 0.7017 (t80) REVERT: B 528 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7940 (tttp) outliers start: 30 outliers final: 19 residues processed: 73 average time/residue: 0.4864 time to fit residues: 37.4478 Evaluate side-chains 70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095564 restraints weight = 10458.323| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.51 r_work: 0.3188 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1833 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= 0.173 Angle : 0.579 12.504 8085 Z= 0.288 Chirality : 0.045 0.151 924 Planarity : 0.004 0.076 1013 Dihedral : 8.058 73.391 870 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.14 % Allowed : 28.41 % 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: 0.11 (0.31), residues: 709 helix: 1.39 (0.34), residues: 223 sheet: -0.78 (0.36), residues: 185 loop : -0.23 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 756 TYR 0.011 0.001 TYR B 776 PHE 0.015 0.002 PHE B 401 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 0.57933 / 0.29 ( 8085) hydrogen bonds : bond 0.03572 / 3.12 ( 255) hydrogen bonds : angle 4.74413 / 3.85 ( 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 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: B 298 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: B 470 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5558 (p90) REVERT: B 528 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7967 (tttp) outliers start: 32 outliers final: 18 residues processed: 76 average time/residue: 0.4669 time to fit residues: 37.4982 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 : 0.228 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 chunk 55 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4034 ------------------------------------------------------------------------------- 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 = 0.123428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096942 restraints weight = 10363.631| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.51 r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5939 Z= 0.118 Angle : 0.549 12.812 8085 Z= 0.272 Chirality : 0.044 0.150 924 Planarity : 0.004 0.075 1013 Dihedral : 7.956 73.383 870 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.37 % Allowed : 30.02 % 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: 0.34 (0.32), residues: 709 helix: 1.80 (0.35), residues: 217 sheet: -0.74 (0.37), residues: 183 loop : -0.17 (0.35), residues: 309 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 0.006 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5939) covalent geometry : angle 0.54853 / 0.27 ( 8085) hydrogen bonds : bond 0.03192 / 2.75 ( 255) hydrogen bonds : angle 4.54966 / 3.71 ( 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: 21 poor density : 50 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: B 298 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: B 428 TYR cc_start: 0.7214 (t80) cc_final: 0.6984 (t80) REVERT: B 470 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5770 (p90) REVERT: B 528 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7963 (tttp) outliers start: 21 outliers final: 14 residues processed: 68 average time/residue: 0.4407 time to fit residues: 31.7299 Evaluate side-chains 66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 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 622 MET 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: 0.9980 chunk 59 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.123977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097430 restraints weight = 10373.788| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.51 r_work: 0.3229 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5939 Z= 0.112 Angle : 0.549 12.678 8085 Z= 0.272 Chirality : 0.043 0.150 924 Planarity : 0.004 0.075 1013 Dihedral : 7.888 73.420 869 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.21 % Allowed : 29.86 % 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: 0.37 (0.31), residues: 709 helix: 1.85 (0.35), residues: 217 sheet: -0.66 (0.37), residues: 180 loop : -0.23 (0.35), residues: 312 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 0.018 0.001 PHE B 401 TRP 0.006 0.001 TRP B 479 HIS 0.003 0.000 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 5939) covalent geometry : angle 0.54867 / 0.27 ( 8085) hydrogen bonds : bond 0.03059 / 2.63 ( 255) hydrogen bonds : angle 4.46311 / 3.63 ( 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 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: B 298 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: B 428 TYR cc_start: 0.7107 (t80) cc_final: 0.6880 (t80) REVERT: B 528 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7965 (tttp) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.4643 time to fit residues: 31.5410 Evaluate side-chains 64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 24 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5308 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096705 restraints weight = 10402.178| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.51 r_work: 0.3222 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5939 Z= 0.133 Angle : 0.548 12.330 8085 Z= 0.270 Chirality : 0.044 0.149 924 Planarity : 0.004 0.077 1013 Dihedral : 7.895 73.400 869 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.05 % Allowed : 30.02 % 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: 0.35 (0.31), residues: 709 helix: 1.81 (0.35), residues: 217 sheet: -0.69 (0.37), residues: 180 loop : -0.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 437 TYR 0.011 0.001 TYR B 776 PHE 0.028 0.002 PHE B 283 TRP 0.008 0.001 TRP B 479 HIS 0.004 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 5939) covalent geometry : angle 0.54847 / 0.27 ( 8085) hydrogen bonds : bond 0.03166 / 2.75 ( 255) hydrogen bonds : angle 4.48286 / 3.64 ( 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 65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: B 298 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7391 (tp30) outliers start: 19 outliers final: 15 residues processed: 61 average time/residue: 0.4824 time to fit residues: 31.1538 Evaluate side-chains 62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 458 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 464 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.122449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095942 restraints weight = 10323.396| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.50 r_work: 0.3193 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2022 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 : 0.576 12.087 8085 Z= 0.286 Chirality : 0.045 0.148 924 Planarity : 0.004 0.076 1013 Dihedral : 7.964 73.363 869 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.21 % Allowed : 29.86 % 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: 0.32 (0.31), residues: 709 helix: 1.72 (0.35), residues: 217 sheet: -0.68 (0.37), residues: 179 loop : -0.20 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 748 TYR 0.014 0.001 TYR B 428 PHE 0.014 0.002 PHE B 648 TRP 0.011 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 0.57578 / 0.29 ( 8085) hydrogen bonds : bond 0.03359 / 2.94 ( 255) hydrogen bonds : angle 4.57889 / 3.70 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.95 seconds wall clock time: 32 minutes 57.37 seconds (1977.37 seconds total)