Starting phenix.real_space_refine on Thu Mar 6 02:47:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoy_33990/03_2025/7yoy_33990.cif" } resolution = 3.64 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= 0.010 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 2859 2.51 5 N 745 2.21 5 O 886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4517 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1095 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "F" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 853 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "I" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 810 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "J" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 831 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Time building chain proxies: 5.21, per 1000 atoms: 1.15 Number of scatterers: 4517 At special positions: 0 Unit cell: (79.356, 102.696, 92.582, 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 886 8.00 N 745 7.00 C 2859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 138 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 216 " distance=2.02 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 208 " distance=1.94 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 567.4 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1070 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 13 sheets defined 2.7% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.654A pdb=" N ALA C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.532A pdb=" N TYR C 140 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.509A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET E 33 " --> pdb=" O THR E 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.509A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET E 33 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 115 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.644A pdb=" N ASP E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.511A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 78 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 76 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 77 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.734A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET F 34 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 39 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.580A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER I 67 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.557A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN I 38 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.971A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.524A pdb=" N ALA J 101 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.877A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER J 67 " --> pdb=" O GLN J 70 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 330 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: 1.17 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 729 1.31 - 1.44: 1395 1.44 - 1.56: 2481 1.56 - 1.69: 0 1.69 - 1.82: 32 Bond restraints: 4637 Sorted by residual: bond pdb=" CA THR J 51 " pdb=" C THR J 51 " ideal model delta sigma weight residual 1.528 1.471 0.056 8.80e-03 1.29e+04 4.12e+01 bond pdb=" C THR J 51 " pdb=" O THR J 51 " ideal model delta sigma weight residual 1.242 1.185 0.056 1.00e-02 1.00e+04 3.19e+01 bond pdb=" CA ALA J 55 " pdb=" C ALA J 55 " ideal model delta sigma weight residual 1.528 1.455 0.073 1.37e-02 5.33e+03 2.84e+01 bond pdb=" C PHE J 62 " pdb=" N ARG J 63 " ideal model delta sigma weight residual 1.331 1.267 0.063 1.24e-02 6.50e+03 2.62e+01 bond pdb=" CA SER J 65 " pdb=" C SER J 65 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.23e-02 6.61e+03 2.20e+01 ... (remaining 4632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 6271 4.39 - 8.77: 47 8.77 - 13.16: 7 13.16 - 17.55: 0 17.55 - 21.93: 1 Bond angle restraints: 6326 Sorted by residual: angle pdb=" N SER J 76 " pdb=" CA SER J 76 " pdb=" C SER J 76 " ideal model delta sigma weight residual 111.14 123.67 -12.53 1.08e+00 8.57e-01 1.35e+02 angle pdb=" N SER J 52 " pdb=" CA SER J 52 " pdb=" C SER J 52 " ideal model delta sigma weight residual 108.41 120.68 -12.27 1.61e+00 3.86e-01 5.80e+01 angle pdb=" N ASN J 53 " pdb=" CA ASN J 53 " pdb=" C ASN J 53 " ideal model delta sigma weight residual 108.76 99.11 9.65 1.58e+00 4.01e-01 3.73e+01 angle pdb=" N LEU J 47 " pdb=" CA LEU J 47 " pdb=" C LEU J 47 " ideal model delta sigma weight residual 111.36 117.60 -6.24 1.09e+00 8.42e-01 3.28e+01 angle pdb=" N PHE J 62 " pdb=" CA PHE J 62 " pdb=" C PHE J 62 " ideal model delta sigma weight residual 109.25 101.38 7.87 1.53e+00 4.27e-01 2.64e+01 ... (remaining 6321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2432 17.44 - 34.87: 213 34.87 - 52.30: 41 52.30 - 69.74: 4 69.74 - 87.17: 3 Dihedral angle restraints: 2693 sinusoidal: 1001 harmonic: 1692 Sorted by residual: dihedral pdb=" CB CYS C 102 " pdb=" SG CYS C 102 " pdb=" SG CYS C 115 " pdb=" CB CYS C 115 " ideal model delta sinusoidal sigma weight residual 93.00 5.83 87.17 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CA ASP I 109 " pdb=" C ASP I 109 " pdb=" N ILE I 110 " pdb=" CA ILE I 110 " ideal model delta harmonic sigma weight residual 180.00 137.56 42.44 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA GLY C 189 " pdb=" C GLY C 189 " pdb=" N SER C 190 " pdb=" CA SER C 190 " ideal model delta harmonic sigma weight residual 180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 ... (remaining 2690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 613 0.091 - 0.183: 79 0.183 - 0.274: 7 0.274 - 0.365: 3 0.365 - 0.456: 1 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA SER J 76 " pdb=" N SER J 76 " pdb=" C SER J 76 " pdb=" CB SER J 76 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CA LEU J 47 " pdb=" N LEU J 47 " pdb=" C LEU J 47 " pdb=" CB LEU J 47 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA SER J 52 " pdb=" N SER J 52 " pdb=" C SER J 52 " pdb=" CB SER J 52 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 700 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 43 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO I 44 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO I 44 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 44 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 90 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO C 91 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 39 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO I 40 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO I 40 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 40 " -0.033 5.00e-02 4.00e+02 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1547 2.82 - 3.34: 3764 3.34 - 3.86: 7332 3.86 - 4.38: 7626 4.38 - 4.90: 13758 Nonbonded interactions: 34027 Sorted by model distance: nonbonded pdb=" O ARG E 9 " pdb=" OG1 THR E 118 " model vdw 2.303 3.040 nonbonded pdb=" OG SER C 221 " pdb=" OH TYR I 30 " model vdw 2.305 3.040 nonbonded pdb=" O ARG I 61 " pdb=" OG SER I 76 " model vdw 2.308 3.040 nonbonded pdb=" O SER I 63 " pdb=" OG1 THR I 74 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR C 100 " pdb=" O ARG C 220 " model vdw 2.334 3.040 ... (remaining 34022 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=0.50 max=1.00 mean=0.99 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: 4.670 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.270 Find NCS groups from input model: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.008 0.073 4637 Z= 0.545 Angle : 1.114 21.934 6326 Z= 0.626 Chirality : 0.065 0.456 703 Planarity : 0.008 0.067 802 Dihedral : 13.197 76.582 1596 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.20 % Allowed : 14.29 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.78 (0.31), residues: 583 helix: -4.27 (0.74), residues: 16 sheet: -1.95 (0.34), residues: 208 loop : -2.90 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 62 HIS 0.003 0.001 HIS I 100 PHE 0.037 0.003 PHE E 108 TYR 0.015 0.002 TYR J 49 ARG 0.004 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 ASN cc_start: 0.8646 (m-40) cc_final: 0.8408 (m110) REVERT: E 85 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8344 (tm-30) REVERT: E 86 ASP cc_start: 0.7505 (m-30) cc_final: 0.6516 (m-30) REVERT: E 106 ASP cc_start: 0.8449 (t70) cc_final: 0.8194 (t70) REVERT: I 22 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8927 (mmtt) REVERT: I 24 GLN cc_start: 0.8424 (mt0) cc_final: 0.7980 (tm-30) REVERT: I 32 ASP cc_start: 0.8323 (t0) cc_final: 0.7979 (t0) REVERT: I 49 TYR cc_start: 0.8586 (p90) cc_final: 0.8290 (p90) REVERT: I 53 ASN cc_start: 0.8061 (t0) cc_final: 0.7585 (t0) REVERT: J 33 LEU cc_start: 0.8642 (mp) cc_final: 0.8209 (mp) REVERT: J 78 LEU cc_start: 0.9304 (mp) cc_final: 0.8828 (mp) REVERT: J 99 TYR cc_start: 0.9266 (p90) cc_final: 0.8747 (p90) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1972 time to fit residues: 34.2970 Evaluate side-chains 112 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079252 restraints weight = 14029.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081659 restraints weight = 7318.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083382 restraints weight = 4784.929| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4637 Z= 0.234 Angle : 0.716 16.006 6326 Z= 0.352 Chirality : 0.042 0.139 703 Planarity : 0.006 0.049 802 Dihedral : 6.642 62.437 647 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.27 % Allowed : 17.55 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.13 (0.32), residues: 583 helix: -2.35 (1.32), residues: 15 sheet: -1.60 (0.34), residues: 218 loop : -2.47 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 62 HIS 0.002 0.001 HIS I 100 PHE 0.018 0.002 PHE E 108 TYR 0.015 0.001 TYR E 104 ARG 0.004 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 ASP cc_start: 0.8776 (p0) cc_final: 0.8548 (p0) REVERT: C 157 ASN cc_start: 0.8350 (m-40) cc_final: 0.8097 (m110) REVERT: E 4 GLU cc_start: 0.9128 (tt0) cc_final: 0.8841 (tt0) REVERT: E 86 ASP cc_start: 0.7514 (m-30) cc_final: 0.7012 (m-30) REVERT: E 104 TYR cc_start: 0.8920 (m-80) cc_final: 0.8667 (m-10) REVERT: I 22 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9038 (mmtm) REVERT: I 49 TYR cc_start: 0.8719 (p90) cc_final: 0.8429 (p90) REVERT: I 53 ASN cc_start: 0.8096 (t0) cc_final: 0.7614 (t0) REVERT: I 72 ILE cc_start: 0.9275 (pt) cc_final: 0.8892 (mm) REVERT: J 33 LEU cc_start: 0.8529 (mp) cc_final: 0.8316 (mp) REVERT: J 54 LEU cc_start: 0.9050 (mp) cc_final: 0.8844 (mp) REVERT: J 99 TYR cc_start: 0.9106 (p90) cc_final: 0.8457 (p90) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.1566 time to fit residues: 27.0127 Evaluate side-chains 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077623 restraints weight = 14122.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080014 restraints weight = 7338.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081690 restraints weight = 4809.144| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4637 Z= 0.249 Angle : 0.704 16.596 6326 Z= 0.340 Chirality : 0.041 0.139 703 Planarity : 0.005 0.048 802 Dihedral : 6.420 62.670 647 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.71 % Allowed : 18.37 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.65 (0.33), residues: 583 helix: -1.60 (1.49), residues: 15 sheet: -1.12 (0.35), residues: 213 loop : -2.26 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 163 HIS 0.002 0.001 HIS I 100 PHE 0.018 0.001 PHE E 108 TYR 0.010 0.001 TYR I 30 ARG 0.003 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: E 86 ASP cc_start: 0.7277 (m-30) cc_final: 0.6567 (m-30) REVERT: E 104 TYR cc_start: 0.8918 (m-80) cc_final: 0.8674 (m-80) REVERT: I 22 LYS cc_start: 0.9399 (mtmm) cc_final: 0.9009 (mmtm) REVERT: I 24 GLN cc_start: 0.8324 (mt0) cc_final: 0.7944 (tm-30) REVERT: I 49 TYR cc_start: 0.8766 (p90) cc_final: 0.8500 (p90) REVERT: I 53 ASN cc_start: 0.8006 (t0) cc_final: 0.7510 (t0) REVERT: I 72 ILE cc_start: 0.9286 (pt) cc_final: 0.8865 (mm) REVERT: J 54 LEU cc_start: 0.9108 (mp) cc_final: 0.8868 (mp) outliers start: 28 outliers final: 18 residues processed: 137 average time/residue: 0.1547 time to fit residues: 26.9784 Evaluate side-chains 129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.089540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076359 restraints weight = 14325.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078734 restraints weight = 7386.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080381 restraints weight = 4869.180| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4637 Z= 0.300 Angle : 0.731 17.574 6326 Z= 0.352 Chirality : 0.042 0.162 703 Planarity : 0.005 0.047 802 Dihedral : 6.446 61.349 647 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 6.12 % Allowed : 19.59 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.45 (0.34), residues: 583 helix: -1.18 (1.56), residues: 15 sheet: -1.07 (0.35), residues: 215 loop : -2.07 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 62 HIS 0.003 0.001 HIS I 100 PHE 0.020 0.002 PHE E 108 TYR 0.009 0.001 TYR I 30 ARG 0.004 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8966 (m-80) cc_final: 0.8712 (m-80) REVERT: E 106 ASP cc_start: 0.8128 (t70) cc_final: 0.7876 (t0) REVERT: I 22 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9167 (mmtt) REVERT: I 24 GLN cc_start: 0.8290 (mt0) cc_final: 0.7870 (tm-30) REVERT: I 49 TYR cc_start: 0.8838 (p90) cc_final: 0.8590 (p90) REVERT: I 53 ASN cc_start: 0.8028 (t0) cc_final: 0.7536 (t0) REVERT: I 72 ILE cc_start: 0.9304 (pt) cc_final: 0.8906 (mp) REVERT: J 54 LEU cc_start: 0.9167 (mp) cc_final: 0.8922 (mp) outliers start: 30 outliers final: 22 residues processed: 127 average time/residue: 0.1585 time to fit residues: 25.7863 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.090035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076967 restraints weight = 14234.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079406 restraints weight = 7127.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081083 restraints weight = 4576.890| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4637 Z= 0.257 Angle : 0.711 17.289 6326 Z= 0.339 Chirality : 0.042 0.137 703 Planarity : 0.005 0.043 802 Dihedral : 6.272 61.659 647 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.31 % Allowed : 22.24 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.35 (0.34), residues: 583 helix: -1.10 (1.53), residues: 15 sheet: -0.97 (0.34), residues: 218 loop : -2.03 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 62 HIS 0.003 0.001 HIS C 191 PHE 0.017 0.001 PHE E 108 TYR 0.008 0.001 TYR I 30 ARG 0.004 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8950 (m-80) cc_final: 0.8629 (m-80) REVERT: E 106 ASP cc_start: 0.8076 (t70) cc_final: 0.7837 (t0) REVERT: I 22 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9167 (mmtt) REVERT: I 24 GLN cc_start: 0.8241 (mt0) cc_final: 0.7819 (tm-30) REVERT: I 49 TYR cc_start: 0.8807 (p90) cc_final: 0.8558 (p90) REVERT: I 53 ASN cc_start: 0.8025 (t0) cc_final: 0.7532 (t0) REVERT: I 72 ILE cc_start: 0.9279 (pt) cc_final: 0.8902 (mp) REVERT: J 54 LEU cc_start: 0.9175 (mp) cc_final: 0.8929 (mp) outliers start: 26 outliers final: 23 residues processed: 125 average time/residue: 0.1595 time to fit residues: 25.2336 Evaluate side-chains 131 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075973 restraints weight = 13975.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078345 restraints weight = 7039.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079988 restraints weight = 4555.082| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4637 Z= 0.302 Angle : 0.735 17.508 6326 Z= 0.349 Chirality : 0.042 0.140 703 Planarity : 0.005 0.039 802 Dihedral : 6.278 60.936 647 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 5.51 % Allowed : 23.06 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.27 (0.34), residues: 583 helix: -1.00 (1.50), residues: 15 sheet: -0.86 (0.34), residues: 217 loop : -2.03 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 62 HIS 0.002 0.001 HIS I 100 PHE 0.019 0.001 PHE E 108 TYR 0.009 0.001 TYR J 36 ARG 0.004 0.001 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8991 (m-80) cc_final: 0.8699 (m-80) REVERT: E 106 ASP cc_start: 0.8071 (t70) cc_final: 0.7815 (t0) REVERT: I 22 LYS cc_start: 0.9397 (mtmm) cc_final: 0.9149 (mmtt) REVERT: I 49 TYR cc_start: 0.8873 (p90) cc_final: 0.8632 (p90) REVERT: I 53 ASN cc_start: 0.8060 (t0) cc_final: 0.7546 (t0) REVERT: I 72 ILE cc_start: 0.9278 (pt) cc_final: 0.8908 (mp) REVERT: I 87 TYR cc_start: 0.8616 (m-80) cc_final: 0.8394 (m-10) outliers start: 27 outliers final: 22 residues processed: 122 average time/residue: 0.1697 time to fit residues: 26.3442 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077394 restraints weight = 13875.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079834 restraints weight = 6943.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081508 restraints weight = 4477.176| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4637 Z= 0.225 Angle : 0.714 16.517 6326 Z= 0.339 Chirality : 0.042 0.139 703 Planarity : 0.005 0.039 802 Dihedral : 6.098 62.009 647 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.90 % Allowed : 23.47 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.11 (0.34), residues: 583 helix: -1.06 (1.45), residues: 15 sheet: -0.72 (0.35), residues: 217 loop : -1.93 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 163 HIS 0.002 0.001 HIS I 100 PHE 0.017 0.001 PHE E 108 TYR 0.008 0.001 TYR J 36 ARG 0.004 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 GLU cc_start: 0.7183 (pm20) cc_final: 0.6883 (pm20) REVERT: E 104 TYR cc_start: 0.8946 (m-80) cc_final: 0.8631 (m-80) REVERT: E 106 ASP cc_start: 0.8053 (t70) cc_final: 0.7823 (t0) REVERT: I 22 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9147 (mmtt) REVERT: I 24 GLN cc_start: 0.8146 (mt0) cc_final: 0.7660 (tm-30) REVERT: I 49 TYR cc_start: 0.8795 (p90) cc_final: 0.8536 (p90) REVERT: I 53 ASN cc_start: 0.8072 (t0) cc_final: 0.7573 (t0) REVERT: I 72 ILE cc_start: 0.9282 (pt) cc_final: 0.8943 (mp) outliers start: 24 outliers final: 19 residues processed: 122 average time/residue: 0.1578 time to fit residues: 24.4058 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.092087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079013 restraints weight = 13672.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081455 restraints weight = 6930.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083120 restraints weight = 4488.555| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4637 Z= 0.188 Angle : 0.683 15.168 6326 Z= 0.326 Chirality : 0.041 0.138 703 Planarity : 0.004 0.042 802 Dihedral : 5.877 64.460 647 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.27 % Allowed : 25.51 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.98 (0.34), residues: 583 helix: -1.05 (1.45), residues: 15 sheet: -0.45 (0.37), residues: 205 loop : -1.94 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 35 HIS 0.001 0.000 HIS I 100 PHE 0.014 0.001 PHE E 108 TYR 0.007 0.001 TYR E 57 ARG 0.004 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8625 (pm20) cc_final: 0.8338 (pm20) REVERT: E 104 TYR cc_start: 0.8870 (m-80) cc_final: 0.8603 (m-80) REVERT: I 22 LYS cc_start: 0.9363 (mtmm) cc_final: 0.9158 (mmtt) REVERT: I 49 TYR cc_start: 0.8727 (p90) cc_final: 0.8456 (p90) REVERT: I 53 ASN cc_start: 0.8037 (t0) cc_final: 0.7544 (t0) REVERT: I 72 ILE cc_start: 0.9275 (pt) cc_final: 0.8986 (mp) REVERT: I 79 GLU cc_start: 0.8963 (tp30) cc_final: 0.8555 (tm-30) outliers start: 16 outliers final: 14 residues processed: 123 average time/residue: 0.1669 time to fit residues: 26.0934 Evaluate side-chains 125 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.092611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079408 restraints weight = 13524.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081883 restraints weight = 7067.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083585 restraints weight = 4610.667| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4637 Z= 0.195 Angle : 0.703 14.647 6326 Z= 0.336 Chirality : 0.041 0.134 703 Planarity : 0.004 0.039 802 Dihedral : 5.844 64.520 647 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.47 % Allowed : 25.10 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.79 (0.34), residues: 583 helix: -1.32 (1.39), residues: 16 sheet: -0.18 (0.39), residues: 193 loop : -1.84 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 46 HIS 0.002 0.001 HIS C 191 PHE 0.016 0.001 PHE E 108 TYR 0.007 0.001 TYR E 57 ARG 0.006 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8598 (pm20) cc_final: 0.8316 (pm20) REVERT: E 5 GLU cc_start: 0.7094 (pm20) cc_final: 0.6869 (pm20) REVERT: E 104 TYR cc_start: 0.8812 (m-80) cc_final: 0.8554 (m-80) REVERT: I 24 GLN cc_start: 0.8114 (mt0) cc_final: 0.7724 (tm-30) REVERT: I 49 TYR cc_start: 0.8723 (p90) cc_final: 0.8442 (p90) REVERT: I 53 ASN cc_start: 0.8075 (t0) cc_final: 0.7572 (t0) REVERT: I 72 ILE cc_start: 0.9257 (pt) cc_final: 0.8985 (mp) REVERT: I 79 GLU cc_start: 0.8956 (tp30) cc_final: 0.8563 (tm-30) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.1698 time to fit residues: 26.5232 Evaluate side-chains 122 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.091523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078374 restraints weight = 13739.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080821 restraints weight = 7054.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082494 restraints weight = 4573.955| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4637 Z= 0.228 Angle : 0.706 15.222 6326 Z= 0.338 Chirality : 0.041 0.154 703 Planarity : 0.005 0.038 802 Dihedral : 5.927 63.521 647 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.06 % Allowed : 25.71 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.86 (0.34), residues: 583 helix: -1.28 (1.39), residues: 16 sheet: -0.34 (0.37), residues: 209 loop : -1.87 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 46 HIS 0.003 0.001 HIS C 191 PHE 0.017 0.001 PHE E 108 TYR 0.007 0.001 TYR J 36 ARG 0.007 0.001 ARG F 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8568 (pm20) cc_final: 0.8276 (pm20) REVERT: E 33 MET cc_start: 0.8841 (mmt) cc_final: 0.8509 (mmm) REVERT: E 104 TYR cc_start: 0.8843 (m-80) cc_final: 0.8593 (m-80) REVERT: I 24 GLN cc_start: 0.8086 (mt0) cc_final: 0.7679 (tm-30) REVERT: I 49 TYR cc_start: 0.8761 (p90) cc_final: 0.8482 (p90) REVERT: I 53 ASN cc_start: 0.8053 (t0) cc_final: 0.7500 (t0) REVERT: I 79 GLU cc_start: 0.8952 (tp30) cc_final: 0.8672 (tm-30) outliers start: 15 outliers final: 14 residues processed: 113 average time/residue: 0.1664 time to fit residues: 23.8469 Evaluate side-chains 119 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN J 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078381 restraints weight = 13945.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080793 restraints weight = 7315.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082472 restraints weight = 4817.376| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4637 Z= 0.231 Angle : 0.717 15.050 6326 Z= 0.345 Chirality : 0.041 0.152 703 Planarity : 0.004 0.038 802 Dihedral : 5.926 63.176 647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.67 % Allowed : 25.31 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.84 (0.34), residues: 583 helix: -1.33 (1.37), residues: 16 sheet: -0.33 (0.37), residues: 209 loop : -1.85 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 46 HIS 0.001 0.001 HIS I 100 PHE 0.017 0.001 PHE E 108 TYR 0.008 0.001 TYR J 36 ARG 0.007 0.001 ARG F 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.42 seconds wall clock time: 40 minutes 4.53 seconds (2404.53 seconds total)