Starting phenix.real_space_refine on Fri Dec 27 14:22:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/12_2024/8d8q_27254.cif" } resolution = 4.2 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= 0.044 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3291 2.51 5 N 874 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5202 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 996 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "L" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.34, per 1000 atoms: 1.60 Number of scatterers: 5202 At special positions: 0 Unit cell: (77.996, 94.86, 102.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1010 8.00 N 874 7.00 C 3291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.12 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.12 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 102 " distance=2.05 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 615.8 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 11.4% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 30B through 30F removed outlier: 4.153A pdb=" N LYS L 30F" --> pdb=" O SER L 30C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.089A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 30 through 31 No H-bonds generated for 'chain 'B' and resid 30 through 31' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.540A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.826A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.707A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.587A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.544A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.551A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.551A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 97 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.116A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 205 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1000 1.32 - 1.45: 1457 1.45 - 1.57: 2834 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 5327 Sorted by residual: bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.449 0.063 2.20e-02 2.07e+03 8.16e+00 bond pdb=" CG ASP H 58 " pdb=" OD1 ASP H 58 " ideal model delta sigma weight residual 1.249 1.198 0.051 1.90e-02 2.77e+03 7.25e+00 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 1.530 1.479 0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CD GLU H 6 " pdb=" OE2 GLU H 6 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.40e+00 ... (remaining 5322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 6105 1.55 - 3.10: 917 3.10 - 4.66: 155 4.66 - 6.21: 41 6.21 - 7.76: 10 Bond angle restraints: 7228 Sorted by residual: angle pdb=" C GLN L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.82e+01 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" C GLY H 104 " pdb=" N PRO H 105 " pdb=" CA PRO H 105 " ideal model delta sigma weight residual 119.56 126.58 -7.02 1.01e+00 9.80e-01 4.83e+01 angle pdb=" C ILE B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta sigma weight residual 119.78 126.73 -6.95 1.03e+00 9.43e-01 4.55e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.47 127.11 -7.64 1.16e+00 7.43e-01 4.34e+01 ... (remaining 7223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3013 16.62 - 33.25: 85 33.25 - 49.87: 24 49.87 - 66.49: 18 66.49 - 83.11: 8 Dihedral angle restraints: 3148 sinusoidal: 1232 harmonic: 1916 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.82 -52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.71 36.29 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.01 -32.01 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 421 0.037 - 0.075: 238 0.075 - 0.112: 88 0.112 - 0.150: 24 0.150 - 0.187: 9 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 777 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.34e+00 pdb=" CG TYR A 489 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " 0.027 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR L 32 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 449 " -0.025 2.00e-02 2.50e+03 1.37e-02 3.74e+00 pdb=" CG TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 449 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 449 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 449 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 449 " -0.021 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 157 2.69 - 3.24: 4892 3.24 - 3.80: 8245 3.80 - 4.35: 11033 4.35 - 4.90: 18057 Nonbonded interactions: 42384 Sorted by model distance: nonbonded pdb=" N TYR L 49 " pdb=" CD1 TYR L 49 " model vdw 2.139 3.420 nonbonded pdb=" O LYS H 111 " pdb=" OH TYR H 114 " model vdw 2.458 3.040 nonbonded pdb=" O TYR L 30A" pdb=" N SER L 30C" model vdw 2.487 3.120 nonbonded pdb=" O SER L 93 " pdb=" OG1 THR L 94 " model vdw 2.490 3.040 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.498 3.120 ... (remaining 42379 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 group one per residue 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: 12.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.280 Find NCS groups from input model: 0.080 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.012 0.066 5327 Z= 0.732 Angle : 1.230 7.760 7228 Z= 0.851 Chirality : 0.054 0.187 780 Planarity : 0.005 0.027 927 Dihedral : 11.021 83.112 1917 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.52 % Favored : 98.33 % Rotamer: Outliers : 0.53 % Allowed : 1.06 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.35), residues: 659 helix: -4.41 (0.31), residues: 33 sheet: 1.24 (0.31), residues: 256 loop : 2.53 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 436 HIS 0.003 0.001 HIS B 90 PHE 0.015 0.004 PHE H 67 TYR 0.030 0.005 TYR A 489 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.6548 (m-80) cc_final: 0.5847 (m-80) REVERT: H 120 LEU cc_start: 0.8426 (tp) cc_final: 0.7602 (pp) REVERT: L 3 VAL cc_start: 0.8346 (t) cc_final: 0.8091 (m) REVERT: L 46 LEU cc_start: 0.8987 (tp) cc_final: 0.8671 (tp) REVERT: L 72 THR cc_start: 0.7216 (m) cc_final: 0.6987 (m) REVERT: L 78 LEU cc_start: 0.8328 (tp) cc_final: 0.7927 (tp) REVERT: L 85 ILE cc_start: 0.8790 (mm) cc_final: 0.8154 (tp) REVERT: A 355 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7329 (ttp-170) REVERT: A 461 LEU cc_start: 0.8715 (mt) cc_final: 0.8506 (mp) REVERT: B 14 SER cc_start: 0.8112 (m) cc_final: 0.7637 (t) REVERT: B 36 TYR cc_start: 0.7400 (m-80) cc_final: 0.6903 (m-80) REVERT: B 46 LEU cc_start: 0.8577 (tp) cc_final: 0.8179 (tp) REVERT: B 47 LEU cc_start: 0.7761 (mp) cc_final: 0.7494 (mt) REVERT: C 18 VAL cc_start: 0.8846 (p) cc_final: 0.8563 (p) REVERT: C 36 TRP cc_start: 0.8957 (m100) cc_final: 0.8585 (m100) REVERT: C 46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7843 (tp30) REVERT: C 51 ILE cc_start: 0.8990 (tt) cc_final: 0.8760 (tt) REVERT: C 70 THR cc_start: 0.8531 (p) cc_final: 0.8182 (t) REVERT: C 72 ASP cc_start: 0.8597 (t0) cc_final: 0.7883 (t70) outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.2525 time to fit residues: 70.8510 Evaluate side-chains 121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5327 Z= 0.190 Angle : 0.643 9.805 7228 Z= 0.348 Chirality : 0.048 0.293 780 Planarity : 0.005 0.039 927 Dihedral : 4.954 19.009 759 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 659 helix: -3.82 (0.58), residues: 33 sheet: 0.59 (0.32), residues: 238 loop : 1.62 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 115 HIS 0.001 0.001 HIS A 519 PHE 0.020 0.002 PHE C 29 TYR 0.017 0.002 TYR L 49 ARG 0.008 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8168 (mmm) cc_final: 0.7936 (mmm) REVERT: H 39 GLN cc_start: 0.7724 (pp30) cc_final: 0.7339 (pp30) REVERT: H 46 GLU cc_start: 0.8233 (tt0) cc_final: 0.7929 (tt0) REVERT: H 111 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7763 (mttt) REVERT: H 113 ASP cc_start: 0.7283 (t70) cc_final: 0.6564 (p0) REVERT: H 120 LEU cc_start: 0.8475 (tp) cc_final: 0.7675 (pp) REVERT: L 3 VAL cc_start: 0.8241 (t) cc_final: 0.8026 (m) REVERT: L 15 LEU cc_start: 0.8361 (mt) cc_final: 0.7715 (mt) REVERT: L 58 VAL cc_start: 0.8473 (t) cc_final: 0.8250 (p) REVERT: L 85 ILE cc_start: 0.8749 (mm) cc_final: 0.8095 (tp) REVERT: L 103 LYS cc_start: 0.8635 (tttt) cc_final: 0.8162 (tptm) REVERT: A 355 ARG cc_start: 0.7497 (ttt90) cc_final: 0.7202 (ttp-170) REVERT: A 398 ASP cc_start: 0.8461 (m-30) cc_final: 0.8222 (m-30) REVERT: A 402 ILE cc_start: 0.8685 (pt) cc_final: 0.8435 (pt) REVERT: A 422 ASN cc_start: 0.9003 (m-40) cc_final: 0.8200 (m-40) REVERT: B 14 SER cc_start: 0.7981 (m) cc_final: 0.7688 (t) REVERT: B 49 TYR cc_start: 0.7774 (p90) cc_final: 0.7547 (p90) REVERT: B 65 SER cc_start: 0.8277 (t) cc_final: 0.7941 (t) REVERT: C 4 LEU cc_start: 0.8098 (mt) cc_final: 0.7619 (mt) REVERT: C 18 VAL cc_start: 0.8665 (p) cc_final: 0.8081 (p) REVERT: C 46 GLU cc_start: 0.8379 (tt0) cc_final: 0.8018 (tp30) REVERT: C 70 THR cc_start: 0.8552 (p) cc_final: 0.8280 (t) REVERT: C 72 ASP cc_start: 0.8600 (t0) cc_final: 0.8006 (t70) REVERT: C 82 LEU cc_start: 0.7984 (tp) cc_final: 0.7614 (tp) REVERT: C 85 GLU cc_start: 0.7903 (pm20) cc_final: 0.7690 (pm20) REVERT: C 104 ASP cc_start: 0.8356 (m-30) cc_final: 0.8016 (m-30) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1975 time to fit residues: 45.4848 Evaluate side-chains 125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5327 Z= 0.185 Angle : 0.597 7.797 7228 Z= 0.325 Chirality : 0.046 0.252 780 Planarity : 0.005 0.039 927 Dihedral : 4.630 19.017 759 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.43 % Favored : 97.42 % Rotamer: Outliers : 0.18 % Allowed : 1.60 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.76 (0.33), residues: 659 helix: -3.63 (0.63), residues: 33 sheet: 0.54 (0.32), residues: 237 loop : 1.07 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.002 0.001 HIS B 90 PHE 0.028 0.002 PHE H 67 TYR 0.018 0.002 TYR L 49 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8260 (mmm) cc_final: 0.7938 (mmm) REVERT: H 39 GLN cc_start: 0.7850 (pp30) cc_final: 0.7314 (pp30) REVERT: H 46 GLU cc_start: 0.8002 (tt0) cc_final: 0.7775 (tt0) REVERT: H 75 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8458 (mmtt) REVERT: H 113 ASP cc_start: 0.7175 (t70) cc_final: 0.6973 (p0) REVERT: H 120 LEU cc_start: 0.8622 (tp) cc_final: 0.7862 (pp) REVERT: L 3 VAL cc_start: 0.8105 (t) cc_final: 0.7888 (m) REVERT: L 48 MET cc_start: 0.7412 (tpp) cc_final: 0.7019 (mmm) REVERT: L 58 VAL cc_start: 0.7956 (t) cc_final: 0.7590 (p) REVERT: L 85 ILE cc_start: 0.8759 (mm) cc_final: 0.8206 (pt) REVERT: L 103 LYS cc_start: 0.8690 (tttt) cc_final: 0.8262 (tptm) REVERT: A 355 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7327 (ttp-170) REVERT: A 357 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7799 (ttm170) REVERT: A 402 ILE cc_start: 0.8688 (pt) cc_final: 0.8415 (pt) REVERT: C 46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8174 (tt0) REVERT: C 47 TRP cc_start: 0.8624 (t60) cc_final: 0.8381 (t60) REVERT: C 70 THR cc_start: 0.8610 (p) cc_final: 0.8299 (t) REVERT: C 71 ARG cc_start: 0.7348 (ppt170) cc_final: 0.7140 (ppt170) REVERT: C 72 ASP cc_start: 0.8627 (t0) cc_final: 0.8026 (t70) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2022 time to fit residues: 41.7613 Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5327 Z= 0.272 Angle : 0.639 9.133 7228 Z= 0.350 Chirality : 0.048 0.313 780 Planarity : 0.005 0.048 927 Dihedral : 4.860 18.817 759 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.42 (0.33), residues: 659 helix: -3.65 (0.73), residues: 27 sheet: 0.30 (0.31), residues: 248 loop : 0.75 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 50 HIS 0.002 0.001 HIS B 90 PHE 0.023 0.002 PHE A 374 TYR 0.031 0.002 TYR H 99 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7865 (pp30) cc_final: 0.7322 (pp30) REVERT: L 3 VAL cc_start: 0.8112 (t) cc_final: 0.7911 (m) REVERT: L 30 LEU cc_start: 0.8530 (tp) cc_final: 0.8236 (tp) REVERT: L 30 TYR cc_start: 0.7973 (t80) cc_final: 0.7615 (t80) REVERT: L 85 ILE cc_start: 0.8749 (mm) cc_final: 0.8254 (pt) REVERT: L 103 LYS cc_start: 0.8684 (tttt) cc_final: 0.8434 (ttpt) REVERT: A 340 GLU cc_start: 0.8860 (mp0) cc_final: 0.8392 (tp30) REVERT: A 355 ARG cc_start: 0.7672 (ttt90) cc_final: 0.7291 (ttp-170) REVERT: A 398 ASP cc_start: 0.8768 (m-30) cc_final: 0.8542 (m-30) REVERT: A 402 ILE cc_start: 0.8848 (pt) cc_final: 0.8620 (pt) REVERT: A 455 LEU cc_start: 0.8370 (tp) cc_final: 0.8130 (tp) REVERT: B 33 LEU cc_start: 0.7818 (tp) cc_final: 0.7556 (tp) REVERT: B 95 ARG cc_start: 0.8485 (mpt-90) cc_final: 0.8258 (mtt-85) REVERT: C 46 GLU cc_start: 0.8371 (tt0) cc_final: 0.8075 (tt0) REVERT: C 47 TRP cc_start: 0.8814 (t60) cc_final: 0.8579 (t60) REVERT: C 72 ASP cc_start: 0.8608 (t0) cc_final: 0.7971 (t70) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1958 time to fit residues: 36.1167 Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5327 Z= 0.242 Angle : 0.625 11.392 7228 Z= 0.342 Chirality : 0.047 0.286 780 Planarity : 0.005 0.043 927 Dihedral : 4.947 18.201 759 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.32), residues: 659 helix: -3.62 (0.77), residues: 27 sheet: 0.44 (0.32), residues: 248 loop : 0.33 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 353 HIS 0.002 0.001 HIS B 90 PHE 0.019 0.002 PHE A 374 TYR 0.028 0.002 TYR H 99 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8162 (mmm) cc_final: 0.7938 (mmm) REVERT: H 46 GLU cc_start: 0.8121 (tt0) cc_final: 0.7726 (tt0) REVERT: L 30 TYR cc_start: 0.8129 (t80) cc_final: 0.7706 (t80) REVERT: L 85 ILE cc_start: 0.8727 (mm) cc_final: 0.8182 (tp) REVERT: A 340 GLU cc_start: 0.8804 (mp0) cc_final: 0.8426 (tp30) REVERT: A 355 ARG cc_start: 0.7745 (ttt90) cc_final: 0.7452 (ttp-170) REVERT: A 402 ILE cc_start: 0.8810 (pt) cc_final: 0.8583 (pt) REVERT: A 409 GLN cc_start: 0.8525 (mp10) cc_final: 0.8167 (mp10) REVERT: A 455 LEU cc_start: 0.8402 (tp) cc_final: 0.8160 (tp) REVERT: B 46 LEU cc_start: 0.8567 (tp) cc_final: 0.8310 (tp) REVERT: C 46 GLU cc_start: 0.8399 (tt0) cc_final: 0.8187 (tt0) REVERT: C 47 TRP cc_start: 0.8856 (t60) cc_final: 0.8611 (t60) REVERT: C 72 ASP cc_start: 0.8661 (t0) cc_final: 0.7931 (t70) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1778 time to fit residues: 33.1666 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 GLN L 30DASN L 30EASN L 37 GLN B 90 HIS C 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 5327 Z= 0.503 Angle : 0.815 11.256 7228 Z= 0.444 Chirality : 0.052 0.291 780 Planarity : 0.006 0.048 927 Dihedral : 5.914 20.174 759 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.42 (0.32), residues: 659 helix: -4.03 (0.53), residues: 27 sheet: 0.17 (0.33), residues: 235 loop : -0.20 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 96 HIS 0.006 0.003 HIS B 90 PHE 0.017 0.003 PHE H 67 TYR 0.040 0.003 TYR H 99 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.6692 (m-80) cc_final: 0.5957 (m-80) REVERT: L 30 TYR cc_start: 0.8520 (t80) cc_final: 0.8217 (t80) REVERT: L 103 LYS cc_start: 0.8691 (tttt) cc_final: 0.8178 (tptm) REVERT: A 340 GLU cc_start: 0.8701 (mp0) cc_final: 0.8234 (tp30) REVERT: A 355 ARG cc_start: 0.7612 (ttt90) cc_final: 0.7169 (ttp-170) REVERT: A 402 ILE cc_start: 0.9075 (pt) cc_final: 0.8864 (pt) REVERT: A 455 LEU cc_start: 0.8713 (tp) cc_final: 0.8364 (tp) REVERT: B 46 LEU cc_start: 0.8635 (tp) cc_final: 0.8363 (tp) REVERT: C 71 ARG cc_start: 0.7700 (ppt170) cc_final: 0.7498 (ppt170) REVERT: C 72 ASP cc_start: 0.8650 (t0) cc_final: 0.7809 (t70) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1884 time to fit residues: 28.9554 Evaluate side-chains 88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30DASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30EASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5327 Z= 0.198 Angle : 0.638 9.367 7228 Z= 0.348 Chirality : 0.047 0.216 780 Planarity : 0.005 0.047 927 Dihedral : 5.275 23.656 759 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.41 (0.32), residues: 659 helix: -3.98 (0.56), residues: 27 sheet: 0.28 (0.34), residues: 237 loop : -0.29 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.001 0.000 HIS B 90 PHE 0.017 0.001 PHE B 71 TYR 0.029 0.002 TYR H 99 ARG 0.012 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.6351 (m-80) cc_final: 0.5891 (m-80) REVERT: L 30 TYR cc_start: 0.8377 (t80) cc_final: 0.7952 (t80) REVERT: L 103 LYS cc_start: 0.8642 (tttt) cc_final: 0.8104 (tptt) REVERT: A 340 GLU cc_start: 0.8657 (mp0) cc_final: 0.8178 (tp30) REVERT: A 455 LEU cc_start: 0.8481 (tp) cc_final: 0.8240 (tp) REVERT: B 46 LEU cc_start: 0.8508 (tp) cc_final: 0.8191 (tp) REVERT: C 10 GLU cc_start: 0.7710 (pp20) cc_final: 0.7396 (pp20) REVERT: C 72 ASP cc_start: 0.8653 (t0) cc_final: 0.8089 (t70) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1879 time to fit residues: 30.0290 Evaluate side-chains 88 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 49 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30DASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30EASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5327 Z= 0.159 Angle : 0.602 6.407 7228 Z= 0.328 Chirality : 0.046 0.196 780 Planarity : 0.005 0.050 927 Dihedral : 5.011 22.409 759 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.44 (0.32), residues: 659 helix: -3.83 (0.63), residues: 27 sheet: 0.21 (0.33), residues: 243 loop : -0.29 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.010 0.003 HIS B 90 PHE 0.013 0.001 PHE A 400 TYR 0.024 0.002 TYR H 99 ARG 0.012 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8135 (tt0) cc_final: 0.7758 (tt0) REVERT: L 30 TYR cc_start: 0.8303 (t80) cc_final: 0.7862 (t80) REVERT: L 103 LYS cc_start: 0.8569 (tttt) cc_final: 0.8076 (tptt) REVERT: A 340 GLU cc_start: 0.8606 (mp0) cc_final: 0.8128 (tp30) REVERT: A 402 ILE cc_start: 0.8815 (pt) cc_final: 0.8600 (pt) REVERT: A 455 LEU cc_start: 0.8422 (tp) cc_final: 0.8202 (tp) REVERT: B 46 LEU cc_start: 0.8455 (tp) cc_final: 0.8254 (tp) REVERT: B 71 PHE cc_start: 0.7623 (m-80) cc_final: 0.7158 (m-80) REVERT: C 46 GLU cc_start: 0.8362 (tt0) cc_final: 0.8119 (tt0) REVERT: C 58 ASN cc_start: 0.7074 (m-40) cc_final: 0.6844 (t0) REVERT: C 61 GLN cc_start: 0.8904 (mt0) cc_final: 0.8274 (mp10) REVERT: C 72 ASP cc_start: 0.8837 (t0) cc_final: 0.8280 (t70) REVERT: C 73 MET cc_start: 0.7634 (pmm) cc_final: 0.7106 (ppp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1766 time to fit residues: 30.7103 Evaluate side-chains 91 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30DASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30EASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5327 Z= 0.192 Angle : 0.619 6.838 7228 Z= 0.331 Chirality : 0.046 0.178 780 Planarity : 0.005 0.053 927 Dihedral : 4.874 22.860 759 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.32), residues: 659 helix: -3.71 (0.69), residues: 27 sheet: 0.42 (0.34), residues: 237 loop : -0.44 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.004 0.001 HIS B 90 PHE 0.016 0.001 PHE H 67 TYR 0.021 0.002 TYR H 99 ARG 0.014 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8543 (mppt) cc_final: 0.8188 (mmtm) REVERT: H 46 GLU cc_start: 0.7910 (tt0) cc_final: 0.7578 (tt0) REVERT: L 30 TYR cc_start: 0.8295 (t80) cc_final: 0.8052 (t80) REVERT: L 92 TYR cc_start: 0.8198 (t80) cc_final: 0.7843 (t80) REVERT: L 103 LYS cc_start: 0.8654 (tttt) cc_final: 0.8129 (tptt) REVERT: A 340 GLU cc_start: 0.8612 (mp0) cc_final: 0.8110 (tp30) REVERT: A 402 ILE cc_start: 0.8869 (pt) cc_final: 0.8667 (pt) REVERT: A 455 LEU cc_start: 0.8466 (tp) cc_final: 0.8258 (tp) REVERT: B 36 TYR cc_start: 0.8114 (m-10) cc_final: 0.7904 (m-10) REVERT: C 46 GLU cc_start: 0.8235 (tt0) cc_final: 0.7952 (tt0) REVERT: C 61 GLN cc_start: 0.8901 (mt0) cc_final: 0.8188 (mp10) REVERT: C 72 ASP cc_start: 0.8600 (t0) cc_final: 0.7836 (t70) REVERT: C 73 MET cc_start: 0.7483 (pmm) cc_final: 0.7142 (ppp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2053 time to fit residues: 32.1627 Evaluate side-chains 91 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30DASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30EASN B 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5327 Z= 0.190 Angle : 0.624 9.110 7228 Z= 0.332 Chirality : 0.046 0.188 780 Planarity : 0.005 0.070 927 Dihedral : 4.848 22.556 759 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.46 (0.32), residues: 659 helix: -3.66 (0.73), residues: 27 sheet: 0.40 (0.34), residues: 237 loop : -0.46 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 50 HIS 0.001 0.001 HIS B 90 PHE 0.030 0.002 PHE H 67 TYR 0.019 0.001 TYR H 99 ARG 0.014 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8497 (mppt) cc_final: 0.8148 (mmtm) REVERT: H 46 GLU cc_start: 0.7919 (tt0) cc_final: 0.7549 (tt0) REVERT: H 120 LEU cc_start: 0.8739 (mm) cc_final: 0.8270 (pp) REVERT: L 70 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8432 (mm-30) REVERT: L 92 TYR cc_start: 0.8196 (t80) cc_final: 0.7954 (t80) REVERT: L 103 LYS cc_start: 0.8661 (tttt) cc_final: 0.8150 (tptt) REVERT: A 340 GLU cc_start: 0.8615 (mp0) cc_final: 0.8113 (tp30) REVERT: A 402 ILE cc_start: 0.8879 (pt) cc_final: 0.8670 (pt) REVERT: A 455 LEU cc_start: 0.8469 (tp) cc_final: 0.8243 (tp) REVERT: A 468 ILE cc_start: 0.8877 (pt) cc_final: 0.8555 (mm) REVERT: B 36 TYR cc_start: 0.8097 (m-10) cc_final: 0.7835 (m-10) REVERT: C 10 GLU cc_start: 0.7895 (pp20) cc_final: 0.7505 (pp20) REVERT: C 61 GLN cc_start: 0.8880 (mt0) cc_final: 0.8364 (mp10) REVERT: C 72 ASP cc_start: 0.8597 (t0) cc_final: 0.7785 (t70) REVERT: C 73 MET cc_start: 0.7455 (pmm) cc_final: 0.7123 (ppp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1883 time to fit residues: 30.5248 Evaluate side-chains 92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 30DASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30EASN B 90 HIS C 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.078462 restraints weight = 18496.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080597 restraints weight = 10998.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082114 restraints weight = 7648.437| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5327 Z= 0.172 Angle : 0.609 7.494 7228 Z= 0.323 Chirality : 0.045 0.172 780 Planarity : 0.005 0.058 927 Dihedral : 4.787 22.464 759 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.52 (0.32), residues: 659 helix: -3.61 (0.74), residues: 27 sheet: 0.31 (0.34), residues: 233 loop : -0.46 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.002 0.001 HIS B 90 PHE 0.017 0.001 PHE H 67 TYR 0.018 0.001 TYR H 99 ARG 0.014 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.17 seconds wall clock time: 36 minutes 30.39 seconds (2190.39 seconds total)