Starting phenix.real_space_refine on Sat May 10 01:40:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoy_33990/05_2025/7yoy_33990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoy_33990/05_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_33990/05_2025/7yoy_33990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoy_33990/05_2025/7yoy_33990.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoy_33990/05_2025/7yoy_33990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoy_33990/05_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-5687/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: 4.42, per 1000 atoms: 0.98 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: 1.03 Conformation dependent library (CDL) restraints added in 563.0 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: 0.61 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: 1.14 Time building geometry restraints manager: 1.24 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: 7.380 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- 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 : 0.511 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: 0.1976 time to fit residues: 34.3010 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 : 0.471 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.092493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079463 restraints weight = 14024.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081875 restraints weight = 7307.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083592 restraints weight = 4773.495| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4646 Z= 0.152 Angle : 0.718 15.912 6344 Z= 0.353 Chirality : 0.042 0.139 703 Planarity : 0.006 0.048 802 Dihedral : 6.632 62.463 647 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.27 % Allowed : 17.76 % Favored : 78.98 % 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: -3.10 (0.32), residues: 583 helix: -2.24 (1.35), residues: 15 sheet: -1.57 (0.34), residues: 218 loop : -2.46 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 62 HIS 0.002 0.001 HIS I 100 PHE 0.017 0.002 PHE E 108 TYR 0.015 0.001 TYR E 104 ARG 0.004 0.001 ARG C 220 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 112) hydrogen bonds : angle 6.81088 ( 330) SS BOND : bond 0.00549 ( 9) SS BOND : angle 1.23675 ( 18) covalent geometry : bond 0.00345 ( 4637) covalent geometry : angle 0.71643 ( 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 : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 ASP cc_start: 0.8770 (p0) cc_final: 0.8528 (p0) REVERT: C 157 ASN cc_start: 0.8356 (m-40) cc_final: 0.8097 (m110) REVERT: E 4 GLU cc_start: 0.9126 (tt0) cc_final: 0.8823 (tt0) REVERT: E 86 ASP cc_start: 0.7535 (m-30) cc_final: 0.7039 (m-30) REVERT: E 104 TYR cc_start: 0.8905 (m-80) cc_final: 0.8610 (m-10) REVERT: I 22 LYS cc_start: 0.9368 (mtmm) cc_final: 0.9036 (mmtm) REVERT: I 49 TYR cc_start: 0.8700 (p90) cc_final: 0.8407 (p90) REVERT: I 53 ASN cc_start: 0.8103 (t0) cc_final: 0.7637 (t0) REVERT: I 72 ILE cc_start: 0.9272 (pt) cc_final: 0.8888 (mm) REVERT: J 33 LEU cc_start: 0.8530 (mp) cc_final: 0.8316 (mp) REVERT: J 99 TYR cc_start: 0.9099 (p90) cc_final: 0.8462 (p90) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.1624 time to fit residues: 27.8833 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 : 0.473 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 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: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.090069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077077 restraints weight = 13873.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079452 restraints weight = 7123.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081119 restraints weight = 4629.436| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | 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: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4646 Z= 0.183 Angle : 0.717 16.655 6344 Z= 0.348 Chirality : 0.041 0.140 703 Planarity : 0.005 0.048 802 Dihedral : 6.468 62.204 647 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % 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: -2.68 (0.33), residues: 583 helix: -1.55 (1.48), residues: 15 sheet: -1.15 (0.35), residues: 213 loop : -2.29 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 62 HIS 0.003 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 C 220 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 112) hydrogen bonds : angle 6.27325 ( 330) SS BOND : bond 0.00548 ( 9) SS BOND : angle 0.98610 ( 18) covalent geometry : bond 0.00424 ( 4637) covalent geometry : angle 0.71654 ( 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 146 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: E 86 ASP cc_start: 0.7286 (m-30) cc_final: 0.6578 (m-30) REVERT: E 104 TYR cc_start: 0.8941 (m-80) cc_final: 0.8712 (m-80) REVERT: I 22 LYS cc_start: 0.9387 (mtmm) cc_final: 0.9005 (mmtm) REVERT: I 24 GLN cc_start: 0.8325 (mt0) cc_final: 0.7935 (tm-30) REVERT: I 49 TYR cc_start: 0.8804 (p90) cc_final: 0.8544 (p90) REVERT: I 53 ASN cc_start: 0.8037 (t0) cc_final: 0.7555 (t0) REVERT: I 72 ILE cc_start: 0.9275 (pt) cc_final: 0.8855 (mm) outliers start: 28 outliers final: 19 residues processed: 134 average time/residue: 0.1560 time to fit residues: 26.5290 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 : 0.489 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.091264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078283 restraints weight = 13929.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080721 restraints weight = 6967.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082416 restraints weight = 4485.270| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 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 = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4646 Z= 0.133 Angle : 0.697 16.896 6344 Z= 0.334 Chirality : 0.042 0.143 703 Planarity : 0.005 0.043 802 Dihedral : 6.257 63.168 647 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.49 % Allowed : 20.20 % Favored : 75.31 % 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: -2.37 (0.34), residues: 583 helix: -1.27 (1.56), residues: 15 sheet: -0.87 (0.36), residues: 204 loop : -2.10 (0.31), residues: 364 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 0.010 0.001 TYR I 30 ARG 0.003 0.001 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 112) hydrogen bonds : angle 5.80723 ( 330) SS BOND : bond 0.00433 ( 9) SS BOND : angle 1.23983 ( 18) covalent geometry : bond 0.00319 ( 4637) covalent geometry : angle 0.69460 ( 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 141 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 SER cc_start: 0.9173 (m) cc_final: 0.8616 (t) REVERT: E 104 TYR cc_start: 0.8938 (m-80) cc_final: 0.8703 (m-80) REVERT: E 106 ASP cc_start: 0.8108 (t70) cc_final: 0.7877 (t0) REVERT: I 22 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9175 (mmtt) REVERT: I 24 GLN cc_start: 0.8261 (mt0) cc_final: 0.7844 (tm-30) REVERT: I 49 TYR cc_start: 0.8747 (p90) cc_final: 0.8475 (p90) REVERT: I 53 ASN cc_start: 0.8001 (t0) cc_final: 0.7507 (t0) REVERT: I 54 LEU cc_start: 0.8472 (mm) cc_final: 0.8238 (mm) REVERT: I 72 ILE cc_start: 0.9297 (pt) cc_final: 0.8920 (mp) outliers start: 22 outliers final: 14 residues processed: 129 average time/residue: 0.1519 time to fit residues: 24.9300 Evaluate side-chains 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 36 VAL 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 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: 0.8980 chunk 19 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.090516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077496 restraints weight = 14117.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079946 restraints weight = 6999.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081627 restraints weight = 4477.482| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 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 = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2776 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= 0.157 Angle : 0.699 16.866 6344 Z= 0.334 Chirality : 0.041 0.139 703 Planarity : 0.005 0.040 802 Dihedral : 6.179 63.036 647 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.90 % Allowed : 22.45 % Favored : 72.65 % 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: -1.30 (1.50), residues: 15 sheet: -0.85 (0.35), residues: 211 loop : -2.01 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 163 HIS 0.002 0.001 HIS C 191 PHE 0.017 0.001 PHE E 108 TYR 0.008 0.001 TYR J 36 ARG 0.007 0.001 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 112) hydrogen bonds : angle 5.63105 ( 330) SS BOND : bond 0.00484 ( 9) SS BOND : angle 1.06359 ( 18) covalent geometry : bond 0.00372 ( 4637) covalent geometry : angle 0.69784 ( 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: 24 poor density : 112 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8950 (m-80) cc_final: 0.8710 (m-80) REVERT: E 106 ASP cc_start: 0.8063 (t70) cc_final: 0.7840 (t0) REVERT: I 22 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9164 (mmtt) REVERT: I 24 GLN cc_start: 0.8236 (mt0) cc_final: 0.7803 (tm-30) REVERT: I 49 TYR cc_start: 0.8782 (p90) cc_final: 0.8526 (p90) REVERT: I 53 ASN cc_start: 0.8014 (t0) cc_final: 0.7536 (t0) REVERT: I 54 LEU cc_start: 0.8472 (mm) cc_final: 0.8241 (mm) REVERT: I 72 ILE cc_start: 0.9293 (pt) cc_final: 0.8953 (mp) outliers start: 24 outliers final: 21 residues processed: 123 average time/residue: 0.1498 time to fit residues: 23.5829 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 THR 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 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 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: 0.7980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 48 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.091655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078815 restraints weight = 13927.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081249 restraints weight = 6947.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082920 restraints weight = 4457.704| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 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 = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2940 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= 0.122 Angle : 0.677 16.347 6344 Z= 0.320 Chirality : 0.041 0.138 703 Planarity : 0.005 0.038 802 Dihedral : 5.954 64.233 647 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.29 % Allowed : 24.08 % 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: -2.09 (0.34), residues: 583 helix: -1.21 (1.49), residues: 15 sheet: -0.60 (0.36), residues: 208 loop : -1.97 (0.31), residues: 360 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 0.015 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 0.03101 ( 112) hydrogen bonds : angle 5.39516 ( 330) SS BOND : bond 0.00419 ( 9) SS BOND : angle 0.91867 ( 18) covalent geometry : bond 0.00294 ( 4637) covalent geometry : angle 0.67596 ( 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 135 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9089 (m) REVERT: E 104 TYR cc_start: 0.8900 (m-80) cc_final: 0.8578 (m-80) REVERT: E 106 ASP cc_start: 0.8066 (t70) cc_final: 0.7863 (t0) REVERT: I 22 LYS cc_start: 0.9373 (mtmm) cc_final: 0.9125 (mmtt) REVERT: I 24 GLN cc_start: 0.8210 (mt0) cc_final: 0.7868 (tm-30) REVERT: I 49 TYR cc_start: 0.8740 (p90) cc_final: 0.8462 (p90) REVERT: I 53 ASN cc_start: 0.8008 (t0) cc_final: 0.7525 (t0) REVERT: I 54 LEU cc_start: 0.8469 (mm) cc_final: 0.8239 (mm) REVERT: I 72 ILE cc_start: 0.9277 (pt) cc_final: 0.8939 (mp) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.1621 time to fit residues: 24.7242 Evaluate side-chains 128 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 overall best weight: 0.5300 ------------------------------------------------------------------------------- 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 = 0.092419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079461 restraints weight = 13848.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081938 restraints weight = 6929.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083605 restraints weight = 4434.019| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 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 = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4646 Z= 0.118 Angle : 0.683 15.565 6344 Z= 0.324 Chirality : 0.041 0.141 703 Planarity : 0.004 0.037 802 Dihedral : 5.822 65.340 647 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.88 % Allowed : 24.69 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.88 (0.34), residues: 583 helix: -1.15 (1.47), residues: 15 sheet: -0.40 (0.37), residues: 200 loop : -1.83 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 163 HIS 0.003 0.001 HIS C 191 PHE 0.014 0.001 PHE E 108 TYR 0.007 0.001 TYR E 57 ARG 0.005 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 112) hydrogen bonds : angle 5.14518 ( 330) SS BOND : bond 0.00397 ( 9) SS BOND : angle 0.99846 ( 18) covalent geometry : bond 0.00286 ( 4637) covalent geometry : angle 0.68190 ( 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 133 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 SER cc_start: 0.9182 (m) cc_final: 0.8595 (t) REVERT: E 104 TYR cc_start: 0.8869 (m-80) cc_final: 0.8585 (m-80) REVERT: I 22 LYS cc_start: 0.9370 (mtmm) cc_final: 0.9153 (mmtt) REVERT: I 24 GLN cc_start: 0.8205 (mt0) cc_final: 0.7821 (tm-30) REVERT: I 49 TYR cc_start: 0.8714 (p90) cc_final: 0.8437 (p90) REVERT: I 53 ASN cc_start: 0.8037 (t0) cc_final: 0.7549 (t0) REVERT: I 72 ILE cc_start: 0.9250 (pt) cc_final: 0.8934 (mp) outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.1537 time to fit residues: 23.4790 Evaluate side-chains 125 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 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 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 22 LYS Chi-restraints excluded: chain J residue 48 ILE 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: 0.9990 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.091988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078872 restraints weight = 13617.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081295 restraints weight = 7021.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082973 restraints weight = 4572.955| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 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 = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4646 Z= 0.138 Angle : 0.694 15.653 6344 Z= 0.334 Chirality : 0.042 0.141 703 Planarity : 0.005 0.036 802 Dihedral : 5.850 64.523 647 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.67 % Allowed : 24.49 % 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: -1.89 (0.34), residues: 583 helix: -1.46 (1.40), residues: 16 sheet: -0.39 (0.37), residues: 207 loop : -1.86 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 163 HIS 0.002 0.000 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 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 112) hydrogen bonds : angle 5.12248 ( 330) SS BOND : bond 0.00427 ( 9) SS BOND : angle 1.03270 ( 18) covalent geometry : bond 0.00330 ( 4637) covalent geometry : angle 0.69330 ( 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 131 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8839 (m-80) cc_final: 0.8541 (m-80) REVERT: I 24 GLN cc_start: 0.8183 (mt0) cc_final: 0.7860 (tm-30) REVERT: I 49 TYR cc_start: 0.8733 (p90) cc_final: 0.8448 (p90) REVERT: I 53 ASN cc_start: 0.8079 (t0) cc_final: 0.7575 (t0) REVERT: I 72 ILE cc_start: 0.9254 (pt) cc_final: 0.8941 (mp) REVERT: I 79 GLU cc_start: 0.8915 (tp30) cc_final: 0.8363 (tm-30) outliers start: 18 outliers final: 16 residues processed: 121 average time/residue: 0.1632 time to fit residues: 25.0568 Evaluate side-chains 124 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 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 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: 0.0670 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.092921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079869 restraints weight = 13632.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082325 restraints weight = 7050.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084013 restraints weight = 4589.954| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4646 Z= 0.119 Angle : 0.709 15.316 6344 Z= 0.342 Chirality : 0.042 0.157 703 Planarity : 0.004 0.036 802 Dihedral : 5.795 65.044 647 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -1.80 (0.34), residues: 583 helix: -1.39 (1.41), residues: 16 sheet: -0.32 (0.38), residues: 196 loop : -1.76 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 163 HIS 0.001 0.000 HIS I 100 PHE 0.015 0.001 PHE E 108 TYR 0.007 0.001 TYR E 57 ARG 0.006 0.000 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 112) hydrogen bonds : angle 5.05192 ( 330) SS BOND : bond 0.00382 ( 9) SS BOND : angle 1.12582 ( 18) covalent geometry : bond 0.00290 ( 4637) covalent geometry : angle 0.70767 ( 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 129 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 TYR cc_start: 0.8794 (m-80) cc_final: 0.8517 (m-80) REVERT: I 24 GLN cc_start: 0.8139 (mt0) cc_final: 0.7838 (tm-30) REVERT: I 49 TYR cc_start: 0.8721 (p90) cc_final: 0.8433 (p90) REVERT: I 53 ASN cc_start: 0.8051 (t0) cc_final: 0.7576 (t0) REVERT: I 72 ILE cc_start: 0.9228 (pt) cc_final: 0.9009 (mp) REVERT: I 79 GLU cc_start: 0.8918 (tp30) cc_final: 0.8469 (tm-30) outliers start: 18 outliers final: 16 residues processed: 119 average time/residue: 0.1552 time to fit residues: 23.6204 Evaluate side-chains 126 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 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 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.091502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078447 restraints weight = 14184.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080819 restraints weight = 7449.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082448 restraints weight = 4906.422| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 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 = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3279 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= 0.165 Angle : 0.725 16.038 6344 Z= 0.350 Chirality : 0.042 0.172 703 Planarity : 0.005 0.035 802 Dihedral : 5.935 63.907 647 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.27 % Allowed : 24.49 % Favored : 72.24 % 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: -1.26 (1.40), residues: 16 sheet: -0.50 (0.36), residues: 212 loop : -1.73 (0.32), residues: 355 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 0.019 0.001 PHE E 108 TYR 0.007 0.001 TYR C 107 ARG 0.007 0.001 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 112) hydrogen bonds : angle 5.09989 ( 330) SS BOND : bond 0.00493 ( 9) SS BOND : angle 1.34094 ( 18) covalent geometry : bond 0.00391 ( 4637) covalent geometry : angle 0.72297 ( 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 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ASP cc_start: 0.8493 (t70) cc_final: 0.8271 (t0) REVERT: E 104 TYR cc_start: 0.8653 (m-80) cc_final: 0.8378 (m-80) REVERT: I 24 GLN cc_start: 0.8175 (mt0) cc_final: 0.7854 (tm-30) REVERT: I 49 TYR cc_start: 0.8757 (p90) cc_final: 0.8506 (p90) REVERT: I 53 ASN cc_start: 0.8070 (t0) cc_final: 0.7540 (t0) REVERT: I 72 ILE cc_start: 0.9245 (pt) cc_final: 0.9021 (mp) outliers start: 16 outliers final: 16 residues processed: 116 average time/residue: 0.1719 time to fit residues: 25.7638 Evaluate side-chains 123 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.091795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078798 restraints weight = 13722.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081202 restraints weight = 6996.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082862 restraints weight = 4547.600| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-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: 6 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4646 Z= 0.142 Angle : 0.720 15.572 6344 Z= 0.345 Chirality : 0.041 0.148 703 Planarity : 0.005 0.037 802 Dihedral : 5.904 63.726 647 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.47 % Allowed : 24.90 % 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: -1.77 (0.34), residues: 583 helix: -1.36 (1.38), residues: 16 sheet: -0.27 (0.37), residues: 204 loop : -1.79 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 46 HIS 0.002 0.001 HIS I 100 PHE 0.017 0.001 PHE E 108 TYR 0.010 0.001 TYR I 87 ARG 0.007 0.001 ARG F 79 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 112) hydrogen bonds : angle 5.08828 ( 330) SS BOND : bond 0.00435 ( 9) SS BOND : angle 1.14514 ( 18) covalent geometry : bond 0.00339 ( 4637) covalent geometry : angle 0.71832 ( 6326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.25 seconds wall clock time: 36 minutes 53.27 seconds (2213.27 seconds total)