Starting phenix.real_space_refine on Wed Jun 11 20:58:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_41299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_41299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_41299.map" model { file = "/net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_41299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tj3_41299/06_2025/8tj3_41299.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.78, per 1000 atoms: 0.67 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.05 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: 5.37 Time building geometry restraints manager: 4.02 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: 24.620 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: 0.210 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.520 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP C 889 HIS 0.006 0.001 HIS C 859 PHE 0.019 0.001 PHE B 315 TYR 0.015 0.001 TYR B 206 ARG 0.010 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.14575 ( 365) hydrogen bonds : angle 6.90991 ( 1062) covalent geometry : bond 0.00403 ( 6620) covalent geometry : angle 0.72288 ( 9006) *********************** 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 : 0.993 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: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.5273 (tpt) cc_final: 0.4984 (tpt) REVERT: C 573 LEU cc_start: 0.7735 (mm) cc_final: 0.7415 (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: 0.3788 (m-80) REVERT: C 838 THR cc_start: 0.7376 (p) cc_final: 0.7123 (t) REVERT: C 839 PRO cc_start: 0.5568 (Cg_exo) cc_final: 0.4736 (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: 0.2579 (tpt) outliers start: 8 outliers final: 2 residues processed: 207 average time/residue: 0.4443 time to fit residues: 120.1463 Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4331 r_free = 0.4331 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.108553 restraints weight = 53791.711| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.15 r_work: 0.3891 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6620 Z= 0.175 Angle : 0.648 8.103 9006 Z= 0.337 Chirality : 0.043 0.165 1047 Planarity : 0.006 0.123 1136 Dihedral : 5.469 66.307 910 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.45 % Allowed : 8.67 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 821 helix: 1.34 (0.25), residues: 459 sheet: -2.04 (0.62), residues: 54 loop : -1.24 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 181 HIS 0.007 0.001 HIS C 987 PHE 0.020 0.002 PHE B 315 TYR 0.014 0.002 TYR C 916 ARG 0.021 0.001 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 365) hydrogen bonds : angle 5.84949 ( 1062) covalent geometry : bond 0.00384 ( 6620) covalent geometry : angle 0.64830 ( 9006) *********************** 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 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.999 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: C 573 LEU cc_start: 0.8074 (mm) cc_final: 0.7670 (pt) REVERT: C 700 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6381 (mp10) REVERT: C 839 PRO cc_start: 0.5624 (Cg_exo) cc_final: 0.5005 (Cg_endo) REVERT: C 896 MET cc_start: 0.3836 (mtp) cc_final: 0.3092 (tpt) outliers start: 10 outliers final: 8 residues processed: 148 average time/residue: 0.3308 time to fit residues: 69.0341 Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 450 ASP 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 911 PHE 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 30 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 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 = 0.4230 r_free = 0.4230 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.100915 restraints weight = 53543.381| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.20 r_work: 0.3752 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6620 Z= 0.219 Angle : 0.682 6.882 9006 Z= 0.355 Chirality : 0.043 0.220 1047 Planarity : 0.005 0.047 1136 Dihedral : 5.660 73.166 910 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.45 % Allowed : 12.14 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 821 helix: 1.29 (0.25), residues: 461 sheet: -2.42 (0.69), residues: 44 loop : -1.60 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 181 HIS 0.013 0.002 HIS C 987 PHE 0.018 0.002 PHE B 315 TYR 0.021 0.002 TYR C 703 ARG 0.020 0.001 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 365) hydrogen bonds : angle 5.34729 ( 1062) covalent geometry : bond 0.00469 ( 6620) covalent geometry : angle 0.68156 ( 9006) *********************** 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 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.146 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: C 573 LEU cc_start: 0.8222 (mm) cc_final: 0.7859 (pt) REVERT: C 862 MET cc_start: 0.6770 (tpp) cc_final: 0.6465 (ttm) REVERT: C 896 MET cc_start: 0.4123 (mtp) cc_final: 0.3040 (tpt) outliers start: 10 outliers final: 7 residues processed: 140 average time/residue: 0.3278 time to fit residues: 64.8661 Evaluate side-chains 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 838 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 966 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.121944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.099617 restraints weight = 51761.175| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.97 r_work: 0.3707 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5448 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= 0.174 Angle : 0.619 6.178 9006 Z= 0.319 Chirality : 0.042 0.153 1047 Planarity : 0.005 0.038 1136 Dihedral : 4.661 46.231 907 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.30 % Allowed : 14.31 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.31), residues: 821 helix: 1.39 (0.25), residues: 460 sheet: -2.33 (0.61), residues: 54 loop : -1.60 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.005 0.001 HIS B 247 PHE 0.021 0.002 PHE B 172 TYR 0.012 0.001 TYR B 317 ARG 0.016 0.001 ARG C 609 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 365) hydrogen bonds : angle 5.22148 ( 1062) covalent geometry : bond 0.00392 ( 6620) covalent geometry : angle 0.61939 ( 9006) *********************** 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 139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.072 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: B 33 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 306 MET cc_start: 0.8600 (tpt) cc_final: 0.8273 (tpt) REVERT: B 350 MET cc_start: 0.8007 (mmt) cc_final: 0.7739 (mmm) REVERT: C 573 LEU cc_start: 0.8278 (mm) cc_final: 0.7910 (pt) REVERT: C 989 MET cc_start: 0.4524 (tmm) cc_final: 0.3918 (ptp) outliers start: 9 outliers final: 8 residues processed: 134 average time/residue: 0.3203 time to fit residues: 60.7680 Evaluate side-chains 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 C residue 447 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 841 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.119837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.096097 restraints weight = 52672.156| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.05 r_work: 0.3651 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6620 Z= 0.166 Angle : 0.613 6.638 9006 Z= 0.314 Chirality : 0.041 0.145 1047 Planarity : 0.004 0.036 1136 Dihedral : 4.572 42.639 907 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.59 % Allowed : 14.60 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 821 helix: 1.55 (0.25), residues: 460 sheet: -2.06 (0.62), residues: 53 loop : -1.64 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 873 HIS 0.005 0.001 HIS B 360 PHE 0.036 0.002 PHE B 172 TYR 0.018 0.002 TYR C 545 ARG 0.005 0.001 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 365) hydrogen bonds : angle 5.02005 ( 1062) covalent geometry : bond 0.00379 ( 6620) covalent geometry : angle 0.61333 ( 9006) *********************** 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 139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.988 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: B 33 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8646 (mp) REVERT: C 573 LEU cc_start: 0.8351 (mm) cc_final: 0.7983 (tp) REVERT: C 862 MET cc_start: 0.7651 (ttm) cc_final: 0.7237 (ttm) REVERT: C 967 ILE cc_start: 0.8080 (mp) cc_final: 0.7786 (tt) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.2826 time to fit residues: 55.8407 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain B residue 346 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 ASN C 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.113678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.089697 restraints weight = 53387.808| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.05 r_work: 0.3513 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6620 Z= 0.284 Angle : 0.712 6.615 9006 Z= 0.380 Chirality : 0.044 0.166 1047 Planarity : 0.005 0.036 1136 Dihedral : 4.831 37.396 907 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.73 % Allowed : 16.76 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 821 helix: 0.97 (0.24), residues: 460 sheet: -2.35 (0.60), residues: 55 loop : -1.84 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 873 HIS 0.007 0.002 HIS B 247 PHE 0.028 0.003 PHE B 315 TYR 0.014 0.002 TYR C 463 ARG 0.011 0.001 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 365) hydrogen bonds : angle 5.35632 ( 1062) covalent geometry : bond 0.00606 ( 6620) covalent geometry : angle 0.71179 ( 9006) *********************** 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 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.059 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 17 ASP cc_start: 0.7245 (t0) cc_final: 0.7028 (t0) REVERT: B 46 MET cc_start: 0.8455 (tpt) cc_final: 0.7944 (tpt) REVERT: C 563 ASP cc_start: 0.8758 (m-30) cc_final: 0.8511 (m-30) REVERT: C 573 LEU cc_start: 0.8495 (mm) cc_final: 0.8217 (tp) REVERT: C 700 GLN cc_start: 0.7911 (mt0) cc_final: 0.7705 (mm-40) REVERT: C 967 ILE cc_start: 0.8310 (mp) cc_final: 0.8023 (tt) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.2911 time to fit residues: 55.7046 Evaluate side-chains 123 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 231 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 627 ILE 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 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.115866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091655 restraints weight = 52563.190| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.95 r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6620 Z= 0.148 Angle : 0.622 6.238 9006 Z= 0.321 Chirality : 0.041 0.142 1047 Planarity : 0.005 0.035 1136 Dihedral : 4.557 35.514 907 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.45 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 821 helix: 1.26 (0.24), residues: 461 sheet: -2.65 (0.56), residues: 56 loop : -1.80 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.004 0.001 HIS B 360 PHE 0.023 0.002 PHE B 315 TYR 0.018 0.002 TYR C 545 ARG 0.003 0.000 ARG C 697 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 365) hydrogen bonds : angle 5.03632 ( 1062) covalent geometry : bond 0.00342 ( 6620) covalent geometry : angle 0.62249 ( 9006) *********************** 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: 10 poor density : 116 time to evaluate : 1.163 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: C 563 ASP cc_start: 0.8751 (m-30) cc_final: 0.8502 (m-30) REVERT: C 573 LEU cc_start: 0.8508 (mm) cc_final: 0.8170 (tp) REVERT: C 581 ASP cc_start: 0.8466 (p0) cc_final: 0.8220 (m-30) REVERT: C 603 GLU cc_start: 0.7564 (mp0) cc_final: 0.7291 (mm-30) REVERT: C 967 ILE cc_start: 0.8281 (mp) cc_final: 0.7976 (tt) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.3314 time to fit residues: 60.0402 Evaluate side-chains 118 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.116048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.091953 restraints weight = 51829.871| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.90 r_work: 0.3563 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.8514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6620 Z= 0.136 Angle : 0.594 6.126 9006 Z= 0.306 Chirality : 0.041 0.138 1047 Planarity : 0.004 0.035 1136 Dihedral : 4.426 32.134 907 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.30 % Allowed : 18.50 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.30), residues: 821 helix: 1.41 (0.24), residues: 460 sheet: -2.39 (0.55), residues: 62 loop : -1.66 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 181 HIS 0.003 0.001 HIS C 859 PHE 0.022 0.002 PHE B 315 TYR 0.015 0.001 TYR C 545 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 365) hydrogen bonds : angle 4.88941 ( 1062) covalent geometry : bond 0.00310 ( 6620) covalent geometry : angle 0.59437 ( 9006) *********************** 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 123 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.936 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: C 563 ASP cc_start: 0.8759 (m-30) cc_final: 0.8505 (m-30) REVERT: C 603 GLU cc_start: 0.7592 (mp0) cc_final: 0.7320 (mm-30) REVERT: C 967 ILE cc_start: 0.8254 (mp) cc_final: 0.7969 (tt) outliers start: 9 outliers final: 9 residues processed: 121 average time/residue: 0.2991 time to fit residues: 52.4230 Evaluate side-chains 118 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 471 LYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 952 THR 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 17 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4050 r_free = 0.4050 target = 0.114953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.090857 restraints weight = 51682.293| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.92 r_work: 0.3538 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.8831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6620 Z= 0.161 Angle : 0.607 5.866 9006 Z= 0.314 Chirality : 0.041 0.135 1047 Planarity : 0.005 0.035 1136 Dihedral : 4.417 31.240 907 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.16 % Allowed : 18.79 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 821 helix: 1.44 (0.24), residues: 460 sheet: -2.34 (0.54), residues: 62 loop : -1.68 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 873 HIS 0.005 0.001 HIS C 859 PHE 0.021 0.002 PHE B 315 TYR 0.017 0.002 TYR C 957 ARG 0.003 0.000 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 365) hydrogen bonds : angle 4.92014 ( 1062) covalent geometry : bond 0.00369 ( 6620) covalent geometry : angle 0.60713 ( 9006) *********************** 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 118 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.232 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 563 ASP cc_start: 0.8750 (m-30) cc_final: 0.8505 (m-30) REVERT: C 568 ASN cc_start: 0.8928 (m-40) cc_final: 0.8624 (m110) REVERT: C 581 ASP cc_start: 0.8556 (p0) cc_final: 0.8227 (m-30) REVERT: C 603 GLU cc_start: 0.7679 (mp0) cc_final: 0.7401 (mm-30) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.4282 time to fit residues: 72.1978 Evaluate side-chains 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 952 THR 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 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.0070 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 63 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 HIS ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092576 restraints weight = 51387.872| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.91 r_work: 0.3571 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.8873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6620 Z= 0.117 Angle : 0.590 5.695 9006 Z= 0.302 Chirality : 0.041 0.139 1047 Planarity : 0.004 0.039 1136 Dihedral : 4.301 29.159 907 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.72 % Allowed : 19.36 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 821 helix: 1.55 (0.24), residues: 461 sheet: -2.28 (0.53), residues: 62 loop : -1.52 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 181 HIS 0.003 0.001 HIS B 362 PHE 0.024 0.002 PHE B 315 TYR 0.010 0.001 TYR C 545 ARG 0.003 0.000 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 365) hydrogen bonds : angle 4.71867 ( 1062) covalent geometry : bond 0.00277 ( 6620) covalent geometry : angle 0.59016 ( 9006) ********************** 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 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.326 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 159 ASP cc_start: 0.8355 (p0) cc_final: 0.7875 (p0) REVERT: C 563 ASP cc_start: 0.8760 (m-30) cc_final: 0.8525 (m-30) REVERT: C 581 ASP cc_start: 0.8515 (p0) cc_final: 0.8194 (m-30) REVERT: C 603 GLU cc_start: 0.7570 (mp0) cc_final: 0.7327 (mm-30) REVERT: C 688 ASN cc_start: 0.8561 (t0) cc_final: 0.8291 (p0) outliers start: 5 outliers final: 3 residues processed: 110 average time/residue: 0.4614 time to fit residues: 79.1064 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 800 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4053 r_free = 0.4053 target = 0.114848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091573 restraints weight = 52408.445| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.93 r_work: 0.3548 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.9100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6620 Z= 0.142 Angle : 0.607 7.241 9006 Z= 0.312 Chirality : 0.040 0.135 1047 Planarity : 0.005 0.037 1136 Dihedral : 4.189 18.526 906 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.58 % Allowed : 19.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 821 helix: 1.61 (0.24), residues: 462 sheet: -2.37 (0.50), residues: 65 loop : -1.52 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 873 HIS 0.003 0.001 HIS C 859 PHE 0.019 0.002 PHE B 315 TYR 0.010 0.001 TYR B 317 ARG 0.003 0.000 ARG C 802 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 365) hydrogen bonds : angle 4.75071 ( 1062) covalent geometry : bond 0.00330 ( 6620) covalent geometry : angle 0.60739 ( 9006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9622.17 seconds wall clock time: 167 minutes 35.60 seconds (10055.60 seconds total)