Starting phenix.real_space_refine on Thu Jun 5 00:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoy_33990/06_2025/7yoy_33990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoy_33990/06_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_33990/06_2025/7yoy_33990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoy_33990/06_2025/7yoy_33990.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoy_33990/06_2025/7yoy_33990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoy_33990/06_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-5710/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: 4.80, per 1000 atoms: 1.06 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: 1.59 Conformation dependent library (CDL) restraints added in 577.8 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: 0.66 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: 1.08 Time building geometry restraints manager: 1.31 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: 5.780 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- 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 0.093 4646 Z= 0.473 Angle : 1.154 24.361 6344 Z= 0.642 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 Details of bonding type rmsd hydrogen bonds : bond 0.28899 ( 112) hydrogen bonds : angle 10.79796 ( 330) SS BOND : bond 0.03167 ( 9) SS BOND : angle 5.80932 ( 18) covalent geometry : bond 0.00807 ( 4637) covalent geometry : angle 1.11360 ( 6326) *********************** 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 : 0.498 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: 0.1981 time to fit residues: 34.4025 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 : 0.529 ------------------------------------------------------------------------------- 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 4646 Z= 0.160 Angle : 0.718 16.006 6344 Z= 0.353 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 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 112) hydrogen bonds : angle 6.82936 ( 330) SS BOND : bond 0.00535 ( 9) SS BOND : angle 1.27413 ( 18) covalent geometry : bond 0.00361 ( 4637) covalent geometry : angle 0.71624 ( 6326) *********************** 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 : 0.476 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: 0.1636 time to fit residues: 28.1868 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 : 0.535 ------------------------------------------------------------------------------- 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: 0.2980 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: 1.0588 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.090562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077433 restraints weight = 14129.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079821 restraints weight = 7356.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081500 restraints weight = 4819.428| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 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 = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4646 Z= 0.171 Angle : 0.708 16.667 6344 Z= 0.342 Chirality : 0.041 0.139 703 Planarity : 0.005 0.048 802 Dihedral : 6.423 62.511 647 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.92 % Allowed : 18.57 % Favored : 75.51 % 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: -2.64 (0.33), residues: 583 helix: -1.59 (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 0.004 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 112) hydrogen bonds : angle 6.20280 ( 330) SS BOND : bond 0.00520 ( 9) SS BOND : angle 0.95472 ( 18) covalent geometry : bond 0.00398 ( 4637) covalent geometry : angle 0.70724 ( 6326) *********************** 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 150 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: E 86 ASP cc_start: 0.7284 (m-30) cc_final: 0.6574 (m-30) REVERT: E 104 TYR cc_start: 0.8926 (m-80) cc_final: 0.8683 (m-80) REVERT: I 22 LYS cc_start: 0.9400 (mtmm) cc_final: 0.9015 (mmtm) REVERT: I 24 GLN cc_start: 0.8321 (mt0) cc_final: 0.7945 (tm-30) REVERT: I 49 TYR cc_start: 0.8772 (p90) cc_final: 0.8507 (p90) REVERT: I 53 ASN cc_start: 0.8009 (t0) cc_final: 0.7519 (t0) REVERT: I 72 ILE cc_start: 0.9286 (pt) cc_final: 0.8870 (mm) REVERT: J 54 LEU cc_start: 0.9115 (mp) cc_final: 0.8870 (mp) outliers start: 29 outliers final: 19 residues processed: 138 average time/residue: 0.1511 time to fit residues: 26.4114 Evaluate side-chains 129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 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 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 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 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: 1.9990 chunk 37 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.091832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078908 restraints weight = 13880.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081380 restraints weight = 6944.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083071 restraints weight = 4431.208| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4646 Z= 0.122 Angle : 0.684 16.624 6344 Z= 0.328 Chirality : 0.042 0.137 703 Planarity : 0.005 0.042 802 Dihedral : 6.162 64.079 647 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.88 % Allowed : 21.02 % Favored : 75.10 % 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: -2.32 (0.34), residues: 583 helix: -1.28 (1.58), residues: 15 sheet: -0.77 (0.37), residues: 195 loop : -2.09 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 174 HIS 0.002 0.000 HIS I 100 PHE 0.015 0.001 PHE E 108 TYR 0.009 0.001 TYR I 30 ARG 0.003 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 112) hydrogen bonds : angle 5.70862 ( 330) SS BOND : bond 0.00401 ( 9) SS BOND : angle 1.16745 ( 18) covalent geometry : bond 0.00294 ( 4637) covalent geometry : angle 0.68178 ( 6326) *********************** 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 137 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 SER cc_start: 0.9164 (m) cc_final: 0.8604 (t) REVERT: E 104 TYR cc_start: 0.8897 (m-80) cc_final: 0.8594 (m-80) REVERT: E 106 ASP cc_start: 0.8086 (t70) cc_final: 0.7881 (t0) REVERT: I 22 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9165 (mmtt) REVERT: I 24 GLN cc_start: 0.8252 (mt0) cc_final: 0.7832 (tm-30) REVERT: I 49 TYR cc_start: 0.8709 (p90) cc_final: 0.8428 (p90) REVERT: I 53 ASN cc_start: 0.7987 (t0) cc_final: 0.7502 (t0) REVERT: I 72 ILE cc_start: 0.9301 (pt) cc_final: 0.8934 (mp) REVERT: J 54 LEU cc_start: 0.9102 (mp) cc_final: 0.8877 (mp) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.1625 time to fit residues: 26.0901 Evaluate side-chains 122 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU 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 58 VAL Chi-restraints excluded: chain I residue 106 THR 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078086 restraints weight = 14135.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080547 restraints weight = 7063.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082243 restraints weight = 4514.823| |-----------------------------------------------------------------------------| 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: 0.8099 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4646 Z= 0.149 Angle : 0.691 16.714 6344 Z= 0.330 Chirality : 0.042 0.140 703 Planarity : 0.005 0.038 802 Dihedral : 6.100 63.858 647 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.29 % Allowed : 22.24 % Favored : 73.47 % 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: -2.24 (0.34), residues: 583 helix: -1.27 (1.53), residues: 15 sheet: -0.81 (0.36), residues: 212 loop : -2.01 (0.32), residues: 356 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 0.016 0.001 PHE E 108 TYR 0.008 0.001 TYR J 36 ARG 0.007 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 112) hydrogen bonds : angle 5.53960 ( 330) SS BOND : bond 0.00450 ( 9) SS BOND : angle 1.10653 ( 18) covalent geometry : bond 0.00355 ( 4637) covalent geometry : angle 0.68934 ( 6326) *********************** 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 136 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: E 36 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9094 (m) REVERT: E 96 SER cc_start: 0.9169 (m) cc_final: 0.8633 (t) REVERT: E 104 TYR cc_start: 0.8920 (m-80) cc_final: 0.8682 (m-80) REVERT: I 22 LYS cc_start: 0.9387 (mtmm) cc_final: 0.9174 (mmtt) REVERT: I 24 GLN cc_start: 0.8240 (mt0) cc_final: 0.7819 (tm-30) REVERT: I 49 TYR cc_start: 0.8754 (p90) cc_final: 0.8467 (p90) REVERT: I 53 ASN cc_start: 0.8010 (t0) cc_final: 0.7528 (t0) REVERT: I 72 ILE cc_start: 0.9275 (pt) cc_final: 0.8937 (mp) REVERT: J 54 LEU cc_start: 0.9129 (mp) cc_final: 0.8909 (mp) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.1491 time to fit residues: 23.5504 Evaluate side-chains 131 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 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 = 0.3500 r_free = 0.3500 target = 0.092173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079310 restraints weight = 13900.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081774 restraints weight = 6932.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083489 restraints weight = 4428.164| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 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 = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4646 Z= 0.119 Angle : 0.670 16.106 6344 Z= 0.319 Chirality : 0.041 0.139 703 Planarity : 0.005 0.037 802 Dihedral : 5.891 64.880 647 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.10 % Allowed : 23.06 % Favored : 71.84 % 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: -2.04 (0.34), residues: 583 helix: -1.21 (1.52), residues: 15 sheet: -0.53 (0.36), residues: 209 loop : -1.95 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 61 HIS 0.002 0.001 HIS I 100 PHE 0.016 0.001 PHE E 108 TYR 0.008 0.001 TYR I 30 ARG 0.005 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 112) hydrogen bonds : angle 5.32405 ( 330) SS BOND : bond 0.00447 ( 9) SS BOND : angle 0.96593 ( 18) covalent geometry : bond 0.00288 ( 4637) covalent geometry : angle 0.66850 ( 6326) *********************** 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 142 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9082 (m) REVERT: E 96 SER cc_start: 0.9184 (m) cc_final: 0.8610 (t) REVERT: E 104 TYR cc_start: 0.8857 (m-80) cc_final: 0.8625 (m-80) REVERT: F 84 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8395 (m) REVERT: I 22 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9173 (mmtt) REVERT: I 24 GLN cc_start: 0.8206 (mt0) cc_final: 0.7844 (tm-30) REVERT: I 49 TYR cc_start: 0.8734 (p90) cc_final: 0.8448 (p90) REVERT: I 53 ASN cc_start: 0.8075 (t0) cc_final: 0.7581 (t0) REVERT: I 72 ILE cc_start: 0.9272 (pt) cc_final: 0.8931 (mp) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 0.1523 time to fit residues: 24.6337 Evaluate side-chains 132 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 84 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.091274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078293 restraints weight = 13887.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080745 restraints weight = 6939.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082439 restraints weight = 4454.202| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 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 = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4646 Z= 0.148 Angle : 0.694 16.156 6344 Z= 0.331 Chirality : 0.041 0.140 703 Planarity : 0.005 0.036 802 Dihedral : 5.903 64.365 647 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.29 % Allowed : 24.49 % 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: -1.89 (0.34), residues: 583 helix: -1.14 (1.47), residues: 15 sheet: -0.46 (0.36), residues: 212 loop : -1.84 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 61 HIS 0.002 0.001 HIS I 100 PHE 0.017 0.001 PHE E 108 TYR 0.007 0.001 TYR J 36 ARG 0.005 0.001 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 112) hydrogen bonds : angle 5.27507 ( 330) SS BOND : bond 0.00432 ( 9) SS BOND : angle 1.03998 ( 18) covalent geometry : bond 0.00353 ( 4637) covalent geometry : angle 0.69309 ( 6326) *********************** 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: 21 poor density : 114 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9104 (m) REVERT: E 104 TYR cc_start: 0.8894 (m-80) cc_final: 0.8566 (m-80) REVERT: I 22 LYS cc_start: 0.9377 (mtmm) cc_final: 0.9102 (mmtp) REVERT: I 24 GLN cc_start: 0.8217 (mt0) cc_final: 0.7811 (tm-30) REVERT: I 49 TYR cc_start: 0.8763 (p90) cc_final: 0.8494 (p90) REVERT: I 53 ASN cc_start: 0.8088 (t0) cc_final: 0.7603 (t0) REVERT: I 72 ILE cc_start: 0.9271 (pt) cc_final: 0.8953 (mp) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.1561 time to fit residues: 24.3346 Evaluate side-chains 127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 52 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.0030 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5568 ------------------------------------------------------------------------------- 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 = 0.092617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079538 restraints weight = 13629.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081992 restraints weight = 7001.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083691 restraints weight = 4545.669| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 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 = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4646 Z= 0.119 Angle : 0.693 15.461 6344 Z= 0.330 Chirality : 0.042 0.140 703 Planarity : 0.004 0.037 802 Dihedral : 5.818 65.190 647 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.29 % Allowed : 24.29 % 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: -1.81 (0.34), residues: 583 helix: -1.02 (1.47), residues: 15 sheet: -0.36 (0.37), residues: 201 loop : -1.79 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 61 HIS 0.001 0.001 HIS I 100 PHE 0.015 0.001 PHE E 108 TYR 0.007 0.001 TYR J 36 ARG 0.004 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 112) hydrogen bonds : angle 5.12466 ( 330) SS BOND : bond 0.00442 ( 9) SS BOND : angle 0.96316 ( 18) covalent geometry : bond 0.00286 ( 4637) covalent geometry : angle 0.69253 ( 6326) *********************** 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 136 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 SER cc_start: 0.9184 (m) cc_final: 0.8631 (t) REVERT: E 104 TYR cc_start: 0.8835 (m-80) cc_final: 0.8564 (m-80) REVERT: I 24 GLN cc_start: 0.8182 (mt0) cc_final: 0.7874 (tm-30) REVERT: I 49 TYR cc_start: 0.8730 (p90) cc_final: 0.8451 (p90) REVERT: I 53 ASN cc_start: 0.8032 (t0) cc_final: 0.7524 (t0) REVERT: I 72 ILE cc_start: 0.9250 (pt) cc_final: 0.8934 (mp) REVERT: I 79 GLU cc_start: 0.8922 (tp30) cc_final: 0.8378 (tm-30) REVERT: I 110 ILE cc_start: 0.0504 (OUTLIER) cc_final: 0.0039 (mm) outliers start: 21 outliers final: 15 residues processed: 123 average time/residue: 0.1585 time to fit residues: 24.5866 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.092517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079507 restraints weight = 13601.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081959 restraints weight = 6994.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083649 restraints weight = 4523.853| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 5 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4646 Z= 0.124 Angle : 0.685 15.264 6344 Z= 0.328 Chirality : 0.041 0.139 703 Planarity : 0.004 0.036 802 Dihedral : 5.752 65.296 647 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.06 % Allowed : 25.10 % Favored : 71.84 % 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: -1.80 (0.34), residues: 583 helix: -1.27 (1.44), residues: 16 sheet: -0.35 (0.37), residues: 201 loop : -1.77 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 46 HIS 0.002 0.000 HIS I 100 PHE 0.015 0.001 PHE E 108 TYR 0.007 0.001 TYR E 57 ARG 0.004 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 112) hydrogen bonds : angle 5.06174 ( 330) SS BOND : bond 0.00431 ( 9) SS BOND : angle 0.95934 ( 18) covalent geometry : bond 0.00301 ( 4637) covalent geometry : angle 0.68412 ( 6326) *********************** 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 130 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 SER cc_start: 0.9190 (m) cc_final: 0.8617 (t) REVERT: E 104 TYR cc_start: 0.8833 (m-80) cc_final: 0.8589 (m-80) REVERT: I 24 GLN cc_start: 0.8161 (mt0) cc_final: 0.7869 (tm-30) REVERT: I 49 TYR cc_start: 0.8720 (p90) cc_final: 0.8442 (p90) REVERT: I 53 ASN cc_start: 0.8073 (t0) cc_final: 0.7581 (t0) REVERT: I 72 ILE cc_start: 0.9230 (pt) cc_final: 0.9025 (mp) REVERT: I 79 GLU cc_start: 0.8936 (tp30) cc_final: 0.8559 (tm-30) outliers start: 15 outliers final: 14 residues processed: 122 average time/residue: 0.1657 time to fit residues: 25.4111 Evaluate side-chains 127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079221 restraints weight = 13570.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081688 restraints weight = 7016.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083412 restraints weight = 4542.241| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4646 Z= 0.134 Angle : 0.704 15.496 6344 Z= 0.336 Chirality : 0.041 0.141 703 Planarity : 0.004 0.036 802 Dihedral : 5.797 64.975 647 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.27 % Allowed : 24.90 % Favored : 71.84 % 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: -1.75 (0.34), residues: 583 helix: -1.28 (1.39), residues: 16 sheet: -0.24 (0.37), residues: 202 loop : -1.78 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 61 HIS 0.001 0.000 HIS I 100 PHE 0.016 0.001 PHE E 108 TYR 0.008 0.001 TYR J 36 ARG 0.004 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 112) hydrogen bonds : angle 5.06799 ( 330) SS BOND : bond 0.00421 ( 9) SS BOND : angle 1.12505 ( 18) covalent geometry : bond 0.00324 ( 4637) covalent geometry : angle 0.70219 ( 6326) ********************** 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 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: E 96 SER cc_start: 0.9193 (m) cc_final: 0.8629 (t) REVERT: E 104 TYR cc_start: 0.8810 (m-80) cc_final: 0.8437 (m-80) REVERT: I 49 TYR cc_start: 0.8722 (p90) cc_final: 0.8448 (p90) REVERT: I 53 ASN cc_start: 0.8058 (t0) cc_final: 0.7524 (t0) REVERT: I 72 ILE cc_start: 0.9241 (pt) cc_final: 0.8972 (tp) REVERT: I 79 GLU cc_start: 0.8953 (tp30) cc_final: 0.8609 (tm-30) outliers start: 16 outliers final: 16 residues processed: 120 average time/residue: 0.1536 time to fit residues: 23.3053 Evaluate side-chains 127 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 101 ASN 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 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 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079109 restraints weight = 13565.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081526 restraints weight = 7062.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083205 restraints weight = 4613.138| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4646 Z= 0.139 Angle : 0.701 15.611 6344 Z= 0.335 Chirality : 0.041 0.141 703 Planarity : 0.004 0.036 802 Dihedral : 5.778 64.807 647 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.88 % Allowed : 24.29 % Favored : 71.84 % 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: -1.72 (0.34), residues: 583 helix: -1.32 (1.38), residues: 16 sheet: -0.16 (0.37), residues: 199 loop : -1.79 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 61 HIS 0.002 0.000 HIS I 100 PHE 0.018 0.001 PHE E 105 TYR 0.007 0.001 TYR E 104 ARG 0.004 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02913 ( 112) hydrogen bonds : angle 5.07419 ( 330) SS BOND : bond 0.00443 ( 9) SS BOND : angle 1.12903 ( 18) covalent geometry : bond 0.00335 ( 4637) covalent geometry : angle 0.69978 ( 6326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.01 seconds wall clock time: 38 minutes 35.47 seconds (2315.47 seconds total)