Starting phenix.real_space_refine on Thu Aug 6 03:16:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tj3_41299/08_2026/8tj3_41299.map" } resolution = 3.2 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 4204 2.51 5 N 1098 2.21 5 O 1142 1.98 5 H 6652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s 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: 13127 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5418 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7709 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 29, 'TRANS': 462} Chain breaks: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.17 Number of scatterers: 13127 At special positions: 0 Unit cell: (80.51, 90.47, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 O 1142 8.00 N 1098 7.00 C 4204 6.00 H 6652 1.00 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: 1.14 Conformation dependent library (CDL) restraints added in 416.7 milliseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 58.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 39 Processing helix chain 'B' and resid 42 through 64 Processing helix chain 'B' and resid 67 through 91 Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 112 through 130 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 140 through 157 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.744A pdb=" N LEU B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 223 through 237 removed outlier: 4.225A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 296 removed outlier: 7.869A pdb=" N LEU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 327 removed outlier: 3.625A pdb=" N ALA B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 363 removed outlier: 4.021A pdb=" N LEU B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 421 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.687A pdb=" N TYR C 427 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 472 removed outlier: 3.917A pdb=" N VAL C 472 " --> pdb=" O PRO C 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 472' Processing helix chain 'C' and resid 474 through 487 Processing helix chain 'C' and resid 489 through 503 Processing helix chain 'C' and resid 516 through 526 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 632 through 644 Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 679 through 688 Processing helix chain 'C' and resid 705 through 708 Processing helix chain 'C' and resid 709 through 720 Processing helix chain 'C' and resid 780 through 789 Processing helix chain 'C' and resid 838 through 851 Processing helix chain 'C' and resid 887 through 901 Processing helix chain 'C' and resid 907 through 911 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 976 through 990 removed outlier: 3.522A pdb=" N LEU C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 438 through 441 removed outlier: 3.674A pdb=" N TYR C 601 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 617 " --> pdb=" O GLU C 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 509 through 512 removed outlier: 3.688A pdb=" N ILE C 509 " --> pdb=" O MET C 467 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 467 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 465 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 460 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 556 through 558 Processing sheet with id=AA4, first strand: chain 'C' and resid 606 through 607 removed outlier: 3.868A pdb=" N ARG C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.715A pdb=" N TYR C 628 " --> pdb=" O MET C 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 662 through 665 365 hydrogen bonds defined for protein. 1062 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: 2.57 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6650 1.03 - 1.23: 19 1.23 - 1.42: 2678 1.42 - 1.62: 3865 1.62 - 1.81: 60 Bond restraints: 13272 Sorted by residual: bond pdb=" N THR C 692 " pdb=" CA THR C 692 " ideal model delta sigma weight residual 1.458 1.484 -0.026 7.40e-03 1.83e+04 1.22e+01 bond pdb=" N ARG C 647 " pdb=" CA ARG C 647 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.22e-02 6.72e+03 1.16e+01 bond pdb=" C ARG C 397 " pdb=" O ARG C 397 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N MET B 203 " pdb=" CA MET B 203 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.94e+00 bond pdb=" C THR B 140 " pdb=" O THR B 140 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.43e-02 4.89e+03 7.47e+00 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 23709 1.93 - 3.85: 332 3.85 - 5.78: 47 5.78 - 7.70: 4 7.70 - 9.63: 2 Bond angle restraints: 24094 Sorted by residual: angle pdb=" CA ARG C 647 " pdb=" C ARG C 647 " pdb=" O ARG C 647 " ideal model delta sigma weight residual 121.16 114.97 6.19 1.12e+00 7.97e-01 3.06e+01 angle pdb=" CA VAL C 652 " pdb=" C VAL C 652 " pdb=" O VAL C 652 " ideal model delta sigma weight residual 121.59 116.60 4.99 1.03e+00 9.43e-01 2.34e+01 angle pdb=" CA ARG C 397 " pdb=" C ARG C 397 " pdb=" O ARG C 397 " ideal model delta sigma weight residual 120.55 115.44 5.11 1.06e+00 8.90e-01 2.33e+01 angle pdb=" CA VAL C 552 " pdb=" C VAL C 552 " pdb=" O VAL C 552 " ideal model delta sigma weight residual 121.18 115.93 5.25 1.16e+00 7.43e-01 2.05e+01 angle pdb=" CA SER C 646 " pdb=" C SER C 646 " pdb=" O SER C 646 " ideal model delta sigma weight residual 120.51 114.07 6.44 1.43e+00 4.89e-01 2.03e+01 ... (remaining 24089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5475 17.72 - 35.44: 479 35.44 - 53.15: 183 53.15 - 70.87: 58 70.87 - 88.59: 16 Dihedral angle restraints: 6211 sinusoidal: 3411 harmonic: 2800 Sorted by residual: dihedral pdb=" CD ARG C 500 " pdb=" NE ARG C 500 " pdb=" CZ ARG C 500 " pdb=" NH1 ARG C 500 " ideal model delta sinusoidal sigma weight residual 0.00 -77.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CD ARG C 502 " pdb=" NE ARG C 502 " pdb=" CZ ARG C 502 " pdb=" NH1 ARG C 502 " ideal model delta sinusoidal sigma weight residual 0.00 50.19 -50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA HIS B 204 " pdb=" C HIS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 748 0.041 - 0.082: 199 0.082 - 0.123: 85 0.123 - 0.164: 13 0.164 - 0.205: 2 Chirality restraints: 1047 Sorted by residual: chirality pdb=" CA VAL C 652 " pdb=" N VAL C 652 " pdb=" C VAL C 652 " pdb=" CB VAL C 652 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL C 552 " pdb=" N VAL C 552 " pdb=" C VAL C 552 " pdb=" CB VAL C 552 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA VAL C 650 " pdb=" N VAL C 650 " pdb=" C VAL C 650 " pdb=" CB VAL C 650 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 1044 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 397 " 0.629 9.50e-02 1.11e+02 4.85e-01 4.35e+03 pdb=" NE ARG C 397 " 0.426 2.00e-02 2.50e+03 pdb=" CZ ARG C 397 " 0.117 2.00e-02 2.50e+03 pdb=" NH1 ARG C 397 " -0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG C 397 " -0.058 2.00e-02 2.50e+03 pdb="HH11 ARG C 397 " -0.697 2.00e-02 2.50e+03 pdb="HH12 ARG C 397 " 0.469 2.00e-02 2.50e+03 pdb="HH21 ARG C 397 " -0.743 2.00e-02 2.50e+03 pdb="HH22 ARG C 397 " 0.513 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 500 " -1.064 9.50e-02 1.11e+02 5.08e-01 3.09e+03 pdb=" NE ARG C 500 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 500 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 500 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG C 500 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG C 500 " -0.233 2.00e-02 2.50e+03 pdb="HH12 ARG C 500 " 0.330 2.00e-02 2.50e+03 pdb="HH21 ARG C 500 " -0.779 2.00e-02 2.50e+03 pdb="HH22 ARG C 500 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 435 " 0.132 9.50e-02 1.11e+02 3.72e-01 3.08e+03 pdb=" NE ARG C 435 " -0.113 2.00e-02 2.50e+03 pdb=" CZ ARG C 435 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 435 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG C 435 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 435 " 0.806 2.00e-02 2.50e+03 pdb="HH12 ARG C 435 " -0.720 2.00e-02 2.50e+03 pdb="HH21 ARG C 435 " 0.165 2.00e-02 2.50e+03 pdb="HH22 ARG C 435 " -0.148 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2667 2.28 - 2.86: 31213 2.86 - 3.44: 36086 3.44 - 4.02: 48169 4.02 - 4.60: 72881 Nonbonded interactions: 191016 Sorted by model distance: nonbonded pdb=" H ARG C 451 " pdb=" O LEU C 631 " model vdw 1.701 2.450 nonbonded pdb=" H THR C 630 " pdb=" O LEU C 860 " model vdw 1.739 2.450 nonbonded pdb=" O ILE B 35 " pdb=" HG SER B 39 " model vdw 1.741 2.450 nonbonded pdb=" H ARG C 435 " pdb=" O VAL C 606 " model vdw 1.757 2.450 nonbonded pdb=" OG1 THR C 630 " pdb=" H VAL C 660 " model vdw 1.767 2.450 ... (remaining 191011 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: 4.750 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: 0.060 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 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 0.042 6620 Z= 0.257 Angle : 0.723 7.944 9006 Z= 0.461 Chirality : 0.045 0.205 1047 Planarity : 0.020 0.481 1136 Dihedral : 13.852 87.650 2410 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.31), residues: 821 helix: 1.43 (0.25), residues: 458 sheet: -2.33 (0.53), residues: 58 loop : -1.48 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 397 TYR 0.015 0.001 TYR B 206 PHE 0.019 0.001 PHE B 315 TRP 0.006 0.001 TRP C 889 HIS 0.006 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.26 ( 6620) covalent geometry : angle 0.72288 / 0.46 ( 9006) hydrogen bonds : bond 0.14575 / 9.47 ( 365) hydrogen bonds : angle 6.90991 / 5.06 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.5273 (tpt) cc_final: 0.4986 (tpt) REVERT: C 573 LEU cc_start: 0.7735 (mm) cc_final: 0.7416 (pt) REVERT: C 609 ARG cc_start: 0.6500 (mpp-170) cc_final: 0.6289 (mmt90) REVERT: C 628 TYR cc_start: 0.4046 (m-80) cc_final: 0.3694 (m-80) REVERT: C 838 THR cc_start: 0.7376 (p) cc_final: 0.7126 (t) REVERT: C 839 PRO cc_start: 0.5568 (Cg_exo) cc_final: 0.4712 (Cg_endo) REVERT: C 871 VAL cc_start: 0.6665 (p) cc_final: 0.5814 (p) REVERT: C 896 MET cc_start: 0.3207 (mtp) cc_final: 0.2578 (tpt) outliers start: 8 outliers final: 2 residues processed: 207 average time/residue: 0.1738 time to fit residues: 47.6398 Evaluate side-chains 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.132122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.110913 restraints weight = 53631.125| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.10 r_work: 0.3939 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6620 Z= 0.150 Angle : 0.655 9.518 9006 Z= 0.337 Chirality : 0.043 0.157 1047 Planarity : 0.006 0.114 1136 Dihedral : 5.450 64.725 910 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.16 % Allowed : 9.25 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 821 helix: 1.36 (0.25), residues: 460 sheet: -1.86 (0.73), residues: 43 loop : -1.31 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 500 TYR 0.013 0.002 TYR C 916 PHE 0.021 0.001 PHE B 315 TRP 0.008 0.001 TRP B 199 HIS 0.003 0.001 HIS C 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6620) covalent geometry : angle 0.65549 / 0.34 ( 9006) hydrogen bonds : bond 0.04294 / 2.72 ( 365) hydrogen bonds : angle 5.74301 / 4.23 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8043 (mm) cc_final: 0.7624 (pt) REVERT: C 628 TYR cc_start: 0.4060 (m-80) cc_final: 0.3770 (m-80) REVERT: C 839 PRO cc_start: 0.5507 (Cg_exo) cc_final: 0.4895 (Cg_endo) REVERT: C 896 MET cc_start: 0.3763 (mtp) cc_final: 0.3120 (tpt) outliers start: 8 outliers final: 7 residues processed: 145 average time/residue: 0.1283 time to fit residues: 27.0010 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain C residue 580 HIS Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 864 THR Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN C 615 GLN ** C 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.122734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.100020 restraints weight = 53535.620| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.04 r_work: 0.3716 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 6620 Z= 0.249 Angle : 0.749 6.980 9006 Z= 0.394 Chirality : 0.045 0.158 1047 Planarity : 0.006 0.075 1136 Dihedral : 5.680 66.395 910 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.73 % Allowed : 11.27 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.24 (0.30), residues: 821 helix: 1.05 (0.24), residues: 461 sheet: -2.33 (0.69), residues: 44 loop : -1.66 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 397 TYR 0.012 0.002 TYR B 317 PHE 0.021 0.002 PHE C 496 TRP 0.012 0.002 TRP B 36 HIS 0.009 0.002 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 ( 6620) covalent geometry : angle 0.74904 / 0.39 ( 9006) hydrogen bonds : bond 0.04592 / 3.02 ( 365) hydrogen bonds : angle 5.38927 / 3.89 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8215 (mm) cc_final: 0.7877 (pt) REVERT: C 581 ASP cc_start: 0.8028 (p0) cc_final: 0.7822 (p0) REVERT: C 700 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6810 (mp10) REVERT: C 702 VAL cc_start: 0.7960 (m) cc_final: 0.7436 (t) REVERT: C 862 MET cc_start: 0.6992 (tpp) cc_final: 0.6671 (ttm) REVERT: C 896 MET cc_start: 0.4200 (mtp) cc_final: 0.3059 (tpt) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.1239 time to fit residues: 26.0233 Evaluate side-chains 131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 841 GLN C 970 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.119849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097944 restraints weight = 52199.447| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.88 r_work: 0.3656 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6620 Z= 0.215 Angle : 0.669 6.107 9006 Z= 0.346 Chirality : 0.044 0.272 1047 Planarity : 0.005 0.075 1136 Dihedral : 5.637 69.135 910 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.73 % Allowed : 15.61 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 821 helix: 1.20 (0.24), residues: 460 sheet: -2.01 (0.66), residues: 50 loop : -1.73 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 802 TYR 0.013 0.002 TYR C 545 PHE 0.013 0.002 PHE B 315 TRP 0.008 0.001 TRP B 245 HIS 0.005 0.001 HIS C 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 6620) covalent geometry : angle 0.66942 / 0.35 ( 9006) hydrogen bonds : bond 0.03928 / 2.57 ( 365) hydrogen bonds : angle 5.21887 / 3.75 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8620 (mp) REVERT: B 306 MET cc_start: 0.8776 (tpt) cc_final: 0.8424 (tpt) REVERT: C 573 LEU cc_start: 0.8330 (mm) cc_final: 0.7969 (tp) REVERT: C 581 ASP cc_start: 0.8133 (p0) cc_final: 0.7836 (p0) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.1166 time to fit residues: 24.2463 Evaluate side-chains 131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 970 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN C 841 GLN C 970 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.119184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095899 restraints weight = 53010.359| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.93 r_work: 0.3626 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6620 Z= 0.177 Angle : 0.612 6.171 9006 Z= 0.317 Chirality : 0.041 0.145 1047 Planarity : 0.004 0.034 1136 Dihedral : 4.680 43.427 907 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.30 % Allowed : 17.34 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.31), residues: 821 helix: 1.35 (0.24), residues: 460 sheet: -2.40 (0.54), residues: 63 loop : -1.70 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 609 TYR 0.014 0.001 TYR C 545 PHE 0.019 0.002 PHE B 315 TRP 0.007 0.001 TRP C 873 HIS 0.005 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6620) covalent geometry : angle 0.61198 / 0.32 ( 9006) hydrogen bonds : bond 0.03750 / 2.45 ( 365) hydrogen bonds : angle 5.06378 / 3.67 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8385 (mm) cc_final: 0.8070 (tp) REVERT: C 700 GLN cc_start: 0.7677 (mt0) cc_final: 0.7087 (mp10) outliers start: 9 outliers final: 8 residues processed: 131 average time/residue: 0.1133 time to fit residues: 22.1040 Evaluate side-chains 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 911 PHE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 970 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN C 841 GLN C 970 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.118312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.094904 restraints weight = 52622.223| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.99 r_work: 0.3606 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6620 Z= 0.168 Angle : 0.602 6.141 9006 Z= 0.313 Chirality : 0.041 0.143 1047 Planarity : 0.004 0.034 1136 Dihedral : 4.594 40.717 907 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.16 % Allowed : 18.21 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.31), residues: 821 helix: 1.41 (0.24), residues: 460 sheet: -2.24 (0.58), residues: 60 loop : -1.71 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.031 0.002 TYR C 910 PHE 0.023 0.001 PHE B 315 TRP 0.006 0.001 TRP C 873 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6620) covalent geometry : angle 0.60184 / 0.31 ( 9006) hydrogen bonds : bond 0.03626 / 2.36 ( 365) hydrogen bonds : angle 4.97161 / 3.62 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 573 LEU cc_start: 0.8468 (mm) cc_final: 0.8149 (tp) REVERT: C 700 GLN cc_start: 0.7633 (mt0) cc_final: 0.6941 (mp10) REVERT: C 967 ILE cc_start: 0.8248 (mp) cc_final: 0.7876 (tt) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.1214 time to fit residues: 22.8926 Evaluate side-chains 123 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.094158 restraints weight = 51525.326| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.75 r_work: 0.3584 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6620 Z= 0.160 Angle : 0.607 7.994 9006 Z= 0.310 Chirality : 0.041 0.132 1047 Planarity : 0.004 0.037 1136 Dihedral : 4.429 33.761 907 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.01 % Allowed : 18.21 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.30), residues: 821 helix: 1.64 (0.24), residues: 454 sheet: -2.26 (0.52), residues: 62 loop : -1.47 (0.38), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 697 TYR 0.020 0.002 TYR C 910 PHE 0.023 0.002 PHE C 523 TRP 0.006 0.001 TRP C 873 HIS 0.005 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6620) covalent geometry : angle 0.60700 / 0.31 ( 9006) hydrogen bonds : bond 0.03373 / 2.20 ( 365) hydrogen bonds : angle 4.76986 / 3.48 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8308 (tpt) cc_final: 0.7956 (tpt) REVERT: C 563 ASP cc_start: 0.8636 (m-30) cc_final: 0.8431 (m-30) REVERT: C 573 LEU cc_start: 0.8469 (mm) cc_final: 0.8095 (tp) REVERT: C 847 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5953 (ttp) REVERT: C 967 ILE cc_start: 0.8201 (mp) cc_final: 0.7960 (tt) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.1162 time to fit residues: 21.7906 Evaluate side-chains 119 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.115626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.093004 restraints weight = 51360.647| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.79 r_work: 0.3551 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.8306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6620 Z= 0.172 Angle : 0.605 6.292 9006 Z= 0.313 Chirality : 0.041 0.135 1047 Planarity : 0.004 0.035 1136 Dihedral : 4.247 17.202 906 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.16 % Allowed : 19.22 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.30), residues: 821 helix: 1.60 (0.24), residues: 455 sheet: -2.39 (0.52), residues: 63 loop : -1.56 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 397 TYR 0.017 0.002 TYR C 910 PHE 0.019 0.002 PHE B 315 TRP 0.005 0.001 TRP C 873 HIS 0.005 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6620) covalent geometry : angle 0.60505 / 0.31 ( 9006) hydrogen bonds : bond 0.03497 / 2.28 ( 365) hydrogen bonds : angle 4.82732 / 3.52 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8341 (tpt) cc_final: 0.7871 (tpt) REVERT: B 203 MET cc_start: 0.6351 (tmm) cc_final: 0.6018 (tmm) REVERT: C 563 ASP cc_start: 0.8645 (m-30) cc_final: 0.8440 (m-30) REVERT: C 847 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6064 (ttp) outliers start: 8 outliers final: 7 residues processed: 123 average time/residue: 0.1244 time to fit residues: 22.8629 Evaluate side-chains 121 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 964 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.116511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.093925 restraints weight = 51393.206| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.81 r_work: 0.3569 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6620 Z= 0.128 Angle : 0.590 6.552 9006 Z= 0.301 Chirality : 0.040 0.153 1047 Planarity : 0.004 0.038 1136 Dihedral : 4.157 17.390 906 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.45 % Allowed : 20.23 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.31), residues: 821 helix: 1.73 (0.24), residues: 455 sheet: -2.36 (0.50), residues: 63 loop : -1.47 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 697 TYR 0.020 0.001 TYR C 916 PHE 0.020 0.001 PHE B 315 TRP 0.005 0.001 TRP B 181 HIS 0.005 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6620) covalent geometry : angle 0.59035 / 0.30 ( 9006) hydrogen bonds : bond 0.03313 / 2.14 ( 365) hydrogen bonds : angle 4.70007 / 3.43 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.8287 (tpt) cc_final: 0.7768 (tpt) REVERT: C 563 ASP cc_start: 0.8636 (m-30) cc_final: 0.8434 (m-30) REVERT: C 581 ASP cc_start: 0.8458 (p0) cc_final: 0.8188 (m-30) REVERT: C 847 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5976 (ttp) REVERT: C 980 LEU cc_start: 0.8447 (mp) cc_final: 0.8233 (mt) outliers start: 10 outliers final: 7 residues processed: 114 average time/residue: 0.1026 time to fit residues: 17.8635 Evaluate side-chains 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 964 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 58 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 37 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.4409 > 50:) overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.117193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094402 restraints weight = 52034.292| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.83 r_work: 0.3580 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.8614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6620 Z= 0.121 Angle : 0.587 6.623 9006 Z= 0.300 Chirality : 0.040 0.164 1047 Planarity : 0.004 0.039 1136 Dihedral : 4.121 17.199 906 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.16 % Allowed : 20.09 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.31), residues: 821 helix: 1.80 (0.24), residues: 455 sheet: -2.46 (0.48), residues: 67 loop : -1.36 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 505 TYR 0.014 0.001 TYR C 910 PHE 0.020 0.001 PHE B 315 TRP 0.005 0.001 TRP B 181 HIS 0.004 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6620) covalent geometry : angle 0.58693 / 0.30 ( 9006) hydrogen bonds : bond 0.03217 / 2.08 ( 365) hydrogen bonds : angle 4.64404 / 3.38 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 ASP cc_start: 0.8387 (p0) cc_final: 0.7922 (p0) REVERT: C 563 ASP cc_start: 0.8576 (m-30) cc_final: 0.8370 (m-30) REVERT: C 581 ASP cc_start: 0.8509 (p0) cc_final: 0.8207 (m-30) REVERT: C 847 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5881 (ttp) REVERT: C 980 LEU cc_start: 0.8443 (mp) cc_final: 0.8237 (mt) outliers start: 8 outliers final: 7 residues processed: 111 average time/residue: 0.1050 time to fit residues: 17.5660 Evaluate side-chains 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 964 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 37 optimal weight: 0.0770 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.116297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.093475 restraints weight = 52228.502| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.75 r_work: 0.3574 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6620 Z= 0.131 Angle : 0.591 7.284 9006 Z= 0.301 Chirality : 0.040 0.147 1047 Planarity : 0.004 0.040 1136 Dihedral : 4.090 16.901 906 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.01 % Allowed : 20.52 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.31), residues: 821 helix: 1.82 (0.24), residues: 456 sheet: -2.38 (0.49), residues: 67 loop : -1.30 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.013 0.001 TYR C 910 PHE 0.025 0.002 PHE C 496 TRP 0.005 0.001 TRP C 873 HIS 0.004 0.001 HIS C 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6620) covalent geometry : angle 0.59146 / 0.30 ( 9006) hydrogen bonds : bond 0.03228 / 2.09 ( 365) hydrogen bonds : angle 4.66039 / 3.40 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.59 seconds wall clock time: 67 minutes 56.16 seconds (4076.16 seconds total)