Starting phenix.real_space_refine on Fri May 9 16:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7j_47678/05_2025/9e7j_47678.cif" } resolution = 2.98 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= 0.021 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 64 5.16 5 C 1912 2.51 5 N 528 2.21 5 O 608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3112 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 778 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Restraints were copied for chains: C, B, D Time building chain proxies: 2.40, per 1000 atoms: 0.77 Number of scatterers: 3112 At special positions: 0 Unit cell: (56.4021, 70.6647, 61.5885, 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 64 16.00 O 608 8.00 N 528 7.00 C 1912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 413.2 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 16 through 42 Processing helix chain 'A' and resid 48 through 71 removed outlier: 3.514A pdb=" N THR A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.196A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 122 removed outlier: 3.599A pdb=" N ALA A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 42 Processing helix chain 'B' and resid 48 through 71 removed outlier: 3.514A pdb=" N THR B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.196A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 122 removed outlier: 3.599A pdb=" N ALA B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 42 Processing helix chain 'C' and resid 48 through 71 removed outlier: 3.514A pdb=" N THR C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 95 removed outlier: 4.196A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 122 removed outlier: 3.599A pdb=" N ALA C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 42 Processing helix chain 'D' and resid 48 through 71 removed outlier: 3.514A pdb=" N THR D 52 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 95 removed outlier: 4.196A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 122 removed outlier: 3.599A pdb=" N ALA D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 888 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: 0.83 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 916 1.33 - 1.45: 388 1.45 - 1.57: 1772 1.57 - 1.68: 0 1.68 - 1.80: 76 Bond restraints: 3152 Sorted by residual: bond pdb=" C CYS D 110 " pdb=" N GLN D 111 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.27e-02 6.20e+03 6.74e+00 bond pdb=" C CYS B 110 " pdb=" N GLN B 111 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.27e-02 6.20e+03 6.74e+00 bond pdb=" C CYS A 110 " pdb=" N GLN A 111 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.27e-02 6.20e+03 6.74e+00 bond pdb=" C CYS C 110 " pdb=" N GLN C 111 " ideal model delta sigma weight residual 1.334 1.367 -0.033 1.27e-02 6.20e+03 6.74e+00 bond pdb=" CB CYS C 26 " pdb=" SG CYS C 26 " ideal model delta sigma weight residual 1.808 1.735 0.073 3.30e-02 9.18e+02 4.85e+00 ... (remaining 3147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 3860 1.44 - 2.87: 316 2.87 - 4.31: 48 4.31 - 5.74: 16 5.74 - 7.18: 4 Bond angle restraints: 4244 Sorted by residual: angle pdb=" N ALA C 54 " pdb=" CA ALA C 54 " pdb=" C ALA C 54 " ideal model delta sigma weight residual 111.28 114.48 -3.20 1.09e+00 8.42e-01 8.59e+00 angle pdb=" N ALA B 54 " pdb=" CA ALA B 54 " pdb=" C ALA B 54 " ideal model delta sigma weight residual 111.28 114.48 -3.20 1.09e+00 8.42e-01 8.59e+00 angle pdb=" N ALA A 54 " pdb=" CA ALA A 54 " pdb=" C ALA A 54 " ideal model delta sigma weight residual 111.28 114.48 -3.20 1.09e+00 8.42e-01 8.59e+00 angle pdb=" N ALA D 54 " pdb=" CA ALA D 54 " pdb=" C ALA D 54 " ideal model delta sigma weight residual 111.28 114.48 -3.20 1.09e+00 8.42e-01 8.59e+00 angle pdb=" C GLN B 111 " pdb=" N ALA B 112 " pdb=" CA ALA B 112 " ideal model delta sigma weight residual 120.28 123.74 -3.46 1.34e+00 5.57e-01 6.65e+00 ... (remaining 4239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 1732 15.72 - 31.43: 148 31.43 - 47.15: 48 47.15 - 62.87: 0 62.87 - 78.58: 8 Dihedral angle restraints: 1936 sinusoidal: 660 harmonic: 1276 Sorted by residual: dihedral pdb=" N MET D 48 " pdb=" CA MET D 48 " pdb=" CB MET D 48 " pdb=" CG MET D 48 " ideal model delta sinusoidal sigma weight residual 180.00 -137.35 -42.65 3 1.50e+01 4.44e-03 7.66e+00 dihedral pdb=" N MET B 48 " pdb=" CA MET B 48 " pdb=" CB MET B 48 " pdb=" CG MET B 48 " ideal model delta sinusoidal sigma weight residual -180.00 -137.35 -42.65 3 1.50e+01 4.44e-03 7.66e+00 dihedral pdb=" N MET C 48 " pdb=" CA MET C 48 " pdb=" CB MET C 48 " pdb=" CG MET C 48 " ideal model delta sinusoidal sigma weight residual -180.00 -137.35 -42.65 3 1.50e+01 4.44e-03 7.66e+00 ... (remaining 1933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 208 0.030 - 0.060: 172 0.060 - 0.089: 80 0.089 - 0.119: 24 0.119 - 0.149: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA THR C 76 " pdb=" N THR C 76 " pdb=" C THR C 76 " pdb=" CB THR C 76 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA THR A 76 " pdb=" N THR A 76 " pdb=" C THR A 76 " pdb=" CB THR A 76 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA THR B 76 " pdb=" N THR B 76 " pdb=" C THR B 76 " pdb=" CB THR B 76 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 489 not shown) Planarity restraints: 552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 76 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO D 77 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 77 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 77 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 76 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO B 77 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO A 77 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.019 5.00e-02 4.00e+02 ... (remaining 549 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1592 2.97 - 3.46: 3394 3.46 - 3.94: 5044 3.94 - 4.42: 6504 4.42 - 4.90: 9876 Nonbonded interactions: 26410 Sorted by model distance: nonbonded pdb=" O LEU A 68 " pdb=" OG1 THR A 76 " model vdw 2.493 3.040 nonbonded pdb=" O LEU B 68 " pdb=" OG1 THR B 76 " model vdw 2.493 3.040 nonbonded pdb=" O LEU C 68 " pdb=" OG1 THR C 76 " model vdw 2.493 3.040 nonbonded pdb=" O LEU D 68 " pdb=" OG1 THR D 76 " model vdw 2.493 3.040 nonbonded pdb=" NZ LYS A 91 " pdb=" OD2 ASP A 95 " model vdw 2.595 3.120 ... (remaining 26405 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.080 Find NCS groups from input model: 0.060 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.011 0.073 3152 Z= 0.500 Angle : 0.898 7.180 4244 Z= 0.528 Chirality : 0.050 0.149 492 Planarity : 0.005 0.033 552 Dihedral : 14.352 78.585 1104 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.37), residues: 432 helix: -0.30 (0.25), residues: 372 sheet: None (None), residues: 0 loop : 0.05 (0.68), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 36 PHE 0.012 0.003 PHE D 97 TYR 0.021 0.003 TYR A 16 ARG 0.000 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.12262 ( 296) hydrogen bonds : angle 5.87766 ( 888) covalent geometry : bond 0.01104 ( 3152) covalent geometry : angle 0.89824 ( 4244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.325 Fit side-chains REVERT: A 43 MET cc_start: 0.7292 (mtt) cc_final: 0.7063 (mtp) REVERT: A 81 LYS cc_start: 0.8452 (tttt) cc_final: 0.8008 (tppt) REVERT: B 43 MET cc_start: 0.7289 (mtt) cc_final: 0.7060 (mtp) REVERT: B 68 LEU cc_start: 0.8328 (mt) cc_final: 0.8123 (mm) REVERT: B 81 LYS cc_start: 0.8456 (tttt) cc_final: 0.8012 (tppt) REVERT: C 43 MET cc_start: 0.7288 (mtt) cc_final: 0.7060 (mtp) REVERT: C 68 LEU cc_start: 0.8314 (mt) cc_final: 0.8109 (mm) REVERT: C 81 LYS cc_start: 0.8456 (tttt) cc_final: 0.8015 (tppt) REVERT: D 43 MET cc_start: 0.7290 (mtt) cc_final: 0.7061 (mtp) REVERT: D 81 LYS cc_start: 0.8452 (tttt) cc_final: 0.8010 (tppt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.4484 time to fit residues: 71.2420 Evaluate side-chains 44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.179020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164090 restraints weight = 2909.303| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.62 r_work: 0.3918 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3152 Z= 0.154 Angle : 0.535 5.795 4244 Z= 0.274 Chirality : 0.035 0.108 492 Planarity : 0.003 0.026 552 Dihedral : 6.963 63.692 452 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 6.96 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.39), residues: 432 helix: 1.20 (0.26), residues: 372 sheet: None (None), residues: 0 loop : 0.65 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 36 PHE 0.006 0.001 PHE B 79 TYR 0.010 0.002 TYR D 16 ARG 0.000 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05334 ( 296) hydrogen bonds : angle 3.46483 ( 888) covalent geometry : bond 0.00320 ( 3152) covalent geometry : angle 0.53472 ( 4244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.304 Fit side-chains REVERT: A 43 MET cc_start: 0.7232 (mtt) cc_final: 0.6937 (mtm) REVERT: A 81 LYS cc_start: 0.8503 (tttt) cc_final: 0.7672 (tppt) REVERT: B 43 MET cc_start: 0.7254 (mtt) cc_final: 0.6956 (mtm) REVERT: B 81 LYS cc_start: 0.8510 (tttt) cc_final: 0.7655 (tppt) REVERT: C 43 MET cc_start: 0.7254 (mtt) cc_final: 0.6956 (mtm) REVERT: C 81 LYS cc_start: 0.8506 (tttt) cc_final: 0.7654 (tppt) REVERT: D 43 MET cc_start: 0.7236 (mtt) cc_final: 0.6941 (mtm) REVERT: D 81 LYS cc_start: 0.8519 (tttt) cc_final: 0.7676 (tppt) outliers start: 8 outliers final: 0 residues processed: 46 average time/residue: 1.2117 time to fit residues: 57.3574 Evaluate side-chains 38 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.174945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161199 restraints weight = 2982.783| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.52 r_work: 0.3921 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3152 Z= 0.164 Angle : 0.528 5.809 4244 Z= 0.268 Chirality : 0.035 0.110 492 Planarity : 0.003 0.024 552 Dihedral : 6.138 54.754 452 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.80 % Allowed : 11.39 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.40), residues: 432 helix: 1.70 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.62 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 36 PHE 0.008 0.001 PHE B 79 TYR 0.010 0.002 TYR D 16 ARG 0.001 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 296) hydrogen bonds : angle 3.35938 ( 888) covalent geometry : bond 0.00355 ( 3152) covalent geometry : angle 0.52791 ( 4244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.306 Fit side-chains REVERT: A 43 MET cc_start: 0.7295 (mtt) cc_final: 0.6952 (mtm) REVERT: A 81 LYS cc_start: 0.8601 (tttt) cc_final: 0.7743 (tppt) REVERT: B 43 MET cc_start: 0.7288 (mtt) cc_final: 0.6950 (mtm) REVERT: B 68 LEU cc_start: 0.7943 (mp) cc_final: 0.7631 (mm) REVERT: B 81 LYS cc_start: 0.8580 (tttt) cc_final: 0.7685 (tppt) REVERT: C 43 MET cc_start: 0.7265 (mtt) cc_final: 0.6925 (mtm) REVERT: C 68 LEU cc_start: 0.7940 (mp) cc_final: 0.7623 (mm) REVERT: C 81 LYS cc_start: 0.8563 (tttt) cc_final: 0.7684 (tppt) REVERT: D 43 MET cc_start: 0.7300 (mtt) cc_final: 0.6955 (mtm) REVERT: D 81 LYS cc_start: 0.8603 (tttt) cc_final: 0.7732 (tppt) outliers start: 12 outliers final: 0 residues processed: 48 average time/residue: 1.3900 time to fit residues: 68.5138 Evaluate side-chains 42 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.175863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161954 restraints weight = 3007.972| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.56 r_work: 0.3933 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3152 Z= 0.154 Angle : 0.513 5.615 4244 Z= 0.259 Chirality : 0.035 0.107 492 Planarity : 0.003 0.023 552 Dihedral : 5.118 42.295 452 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 16.46 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.40), residues: 432 helix: 1.94 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.63 (0.75), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 36 PHE 0.007 0.001 PHE B 79 TYR 0.010 0.002 TYR D 16 ARG 0.001 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05140 ( 296) hydrogen bonds : angle 3.23351 ( 888) covalent geometry : bond 0.00328 ( 3152) covalent geometry : angle 0.51289 ( 4244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.290 Fit side-chains REVERT: A 43 MET cc_start: 0.7327 (mtt) cc_final: 0.6989 (mtm) REVERT: A 81 LYS cc_start: 0.8616 (tttt) cc_final: 0.7773 (tppt) REVERT: B 43 MET cc_start: 0.7339 (mtt) cc_final: 0.6999 (mtm) REVERT: B 68 LEU cc_start: 0.7982 (mp) cc_final: 0.7692 (mm) REVERT: B 81 LYS cc_start: 0.8584 (tttt) cc_final: 0.7709 (tppt) REVERT: C 43 MET cc_start: 0.7306 (mtt) cc_final: 0.6967 (mtm) REVERT: C 68 LEU cc_start: 0.7980 (mp) cc_final: 0.7687 (mm) REVERT: C 81 LYS cc_start: 0.8577 (tttt) cc_final: 0.7708 (tppt) REVERT: D 43 MET cc_start: 0.7332 (mtt) cc_final: 0.6991 (mtm) REVERT: D 81 LYS cc_start: 0.8603 (tttt) cc_final: 0.7748 (tppt) outliers start: 6 outliers final: 0 residues processed: 46 average time/residue: 1.3445 time to fit residues: 63.4807 Evaluate side-chains 42 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.173031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159348 restraints weight = 2957.997| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.53 r_work: 0.3909 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3152 Z= 0.171 Angle : 0.551 6.173 4244 Z= 0.276 Chirality : 0.036 0.107 492 Planarity : 0.003 0.022 552 Dihedral : 4.299 29.443 452 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 18.99 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.40), residues: 432 helix: 1.90 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.71 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 118 PHE 0.009 0.001 PHE B 79 TYR 0.011 0.002 TYR B 16 ARG 0.001 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 296) hydrogen bonds : angle 3.34832 ( 888) covalent geometry : bond 0.00378 ( 3152) covalent geometry : angle 0.55139 ( 4244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.362 Fit side-chains REVERT: A 81 LYS cc_start: 0.8631 (tttt) cc_final: 0.7771 (tppt) REVERT: A 111 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: B 68 LEU cc_start: 0.7968 (mp) cc_final: 0.7698 (mm) REVERT: B 81 LYS cc_start: 0.8641 (tttt) cc_final: 0.7749 (tppt) REVERT: B 111 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: C 68 LEU cc_start: 0.7965 (mp) cc_final: 0.7688 (mm) REVERT: C 81 LYS cc_start: 0.8646 (tttt) cc_final: 0.7758 (tppt) REVERT: C 111 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: D 81 LYS cc_start: 0.8628 (tttt) cc_final: 0.7766 (tppt) REVERT: D 111 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6812 (tt0) outliers start: 6 outliers final: 0 residues processed: 50 average time/residue: 1.4061 time to fit residues: 72.2608 Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 111 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.173411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159450 restraints weight = 3040.099| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.61 r_work: 0.3901 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3152 Z= 0.170 Angle : 0.555 6.386 4244 Z= 0.277 Chirality : 0.036 0.107 492 Planarity : 0.003 0.021 552 Dihedral : 3.783 20.104 452 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 18.99 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.40), residues: 432 helix: 2.06 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.21 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 118 PHE 0.010 0.001 PHE B 79 TYR 0.011 0.002 TYR B 16 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 296) hydrogen bonds : angle 3.34662 ( 888) covalent geometry : bond 0.00374 ( 3152) covalent geometry : angle 0.55516 ( 4244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.323 Fit side-chains REVERT: A 81 LYS cc_start: 0.8599 (tttt) cc_final: 0.7710 (tppt) REVERT: B 68 LEU cc_start: 0.7933 (mp) cc_final: 0.7670 (mm) REVERT: B 81 LYS cc_start: 0.8599 (tttt) cc_final: 0.7689 (tppt) REVERT: B 111 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: C 68 LEU cc_start: 0.7918 (mp) cc_final: 0.7651 (mm) REVERT: C 81 LYS cc_start: 0.8601 (tttt) cc_final: 0.7696 (tppt) REVERT: C 111 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: D 81 LYS cc_start: 0.8595 (tttt) cc_final: 0.7699 (tppt) outliers start: 6 outliers final: 0 residues processed: 48 average time/residue: 1.2706 time to fit residues: 62.7229 Evaluate side-chains 44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 111 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.173306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159492 restraints weight = 2989.903| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.57 r_work: 0.3889 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3152 Z= 0.170 Angle : 0.553 6.316 4244 Z= 0.277 Chirality : 0.036 0.107 492 Planarity : 0.003 0.020 552 Dihedral : 3.500 12.917 452 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.63 % Allowed : 20.89 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.40), residues: 432 helix: 2.07 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.19 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.010 0.001 PHE B 79 TYR 0.011 0.002 TYR B 16 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 296) hydrogen bonds : angle 3.35195 ( 888) covalent geometry : bond 0.00374 ( 3152) covalent geometry : angle 0.55286 ( 4244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.305 Fit side-chains REVERT: A 81 LYS cc_start: 0.8560 (tttt) cc_final: 0.7644 (tppt) REVERT: A 111 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: B 68 LEU cc_start: 0.7825 (mp) cc_final: 0.7575 (mm) REVERT: B 81 LYS cc_start: 0.8555 (tttt) cc_final: 0.7623 (tppt) REVERT: C 68 LEU cc_start: 0.7819 (mp) cc_final: 0.7565 (mm) REVERT: C 81 LYS cc_start: 0.8556 (tttt) cc_final: 0.7626 (tppt) REVERT: D 81 LYS cc_start: 0.8552 (tttt) cc_final: 0.7630 (tppt) REVERT: D 111 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6787 (tt0) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 1.3867 time to fit residues: 65.4824 Evaluate side-chains 44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain D residue 111 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.176030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162375 restraints weight = 2984.609| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.54 r_work: 0.3943 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3152 Z= 0.146 Angle : 0.531 5.975 4244 Z= 0.264 Chirality : 0.034 0.105 492 Planarity : 0.003 0.020 552 Dihedral : 3.283 9.273 452 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.27 % Allowed : 20.25 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.40), residues: 432 helix: 2.31 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.26 (0.77), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 118 PHE 0.008 0.001 PHE B 79 TYR 0.010 0.001 TYR D 16 ARG 0.000 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 296) hydrogen bonds : angle 3.19328 ( 888) covalent geometry : bond 0.00307 ( 3152) covalent geometry : angle 0.53070 ( 4244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.357 Fit side-chains REVERT: A 81 LYS cc_start: 0.8580 (tttt) cc_final: 0.7699 (tppt) REVERT: A 98 PRO cc_start: 0.8452 (Cg_endo) cc_final: 0.8182 (Cg_exo) REVERT: A 111 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: B 68 LEU cc_start: 0.7910 (mp) cc_final: 0.7676 (mm) REVERT: B 81 LYS cc_start: 0.8577 (tttt) cc_final: 0.7675 (tppt) REVERT: B 98 PRO cc_start: 0.8461 (Cg_endo) cc_final: 0.8190 (Cg_exo) REVERT: B 111 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: C 68 LEU cc_start: 0.7903 (mp) cc_final: 0.7664 (mm) REVERT: C 81 LYS cc_start: 0.8574 (tttt) cc_final: 0.7672 (tppt) REVERT: C 98 PRO cc_start: 0.8458 (Cg_endo) cc_final: 0.8188 (Cg_exo) REVERT: C 111 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: D 81 LYS cc_start: 0.8572 (tttt) cc_final: 0.7690 (tppt) REVERT: D 98 PRO cc_start: 0.8456 (Cg_endo) cc_final: 0.8186 (Cg_exo) REVERT: D 111 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6879 (tt0) outliers start: 4 outliers final: 0 residues processed: 50 average time/residue: 1.3245 time to fit residues: 68.0077 Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 111 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.176821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163186 restraints weight = 2972.223| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.56 r_work: 0.3955 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3152 Z= 0.150 Angle : 0.534 5.813 4244 Z= 0.266 Chirality : 0.035 0.103 492 Planarity : 0.003 0.019 552 Dihedral : 3.186 9.428 452 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.27 % Allowed : 21.20 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.40), residues: 432 helix: 2.39 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.22 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 118 PHE 0.009 0.001 PHE C 79 TYR 0.010 0.001 TYR A 16 ARG 0.001 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 296) hydrogen bonds : angle 3.16704 ( 888) covalent geometry : bond 0.00322 ( 3152) covalent geometry : angle 0.53373 ( 4244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.298 Fit side-chains REVERT: A 81 LYS cc_start: 0.8591 (tttt) cc_final: 0.7719 (tppt) REVERT: A 98 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: A 111 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: B 68 LEU cc_start: 0.7937 (mp) cc_final: 0.7705 (mm) REVERT: B 81 LYS cc_start: 0.8586 (tttt) cc_final: 0.7703 (tppt) REVERT: B 98 PRO cc_start: 0.8467 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: B 111 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: C 68 LEU cc_start: 0.7927 (mp) cc_final: 0.7692 (mm) REVERT: C 81 LYS cc_start: 0.8585 (tttt) cc_final: 0.7698 (tppt) REVERT: C 98 PRO cc_start: 0.8467 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: C 111 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: D 81 LYS cc_start: 0.8588 (tttt) cc_final: 0.7709 (tppt) REVERT: D 98 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.8196 (Cg_exo) REVERT: D 111 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6912 (tt0) outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 1.3002 time to fit residues: 69.4471 Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 111 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.183260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.168970 restraints weight = 2813.732| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.61 r_work: 0.4018 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3152 Z= 0.137 Angle : 0.524 5.699 4244 Z= 0.260 Chirality : 0.034 0.102 492 Planarity : 0.002 0.019 552 Dihedral : 3.096 8.939 452 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 21.52 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.40), residues: 432 helix: 2.56 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.21 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 118 PHE 0.008 0.001 PHE C 79 TYR 0.008 0.001 TYR A 16 ARG 0.000 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 296) hydrogen bonds : angle 3.04429 ( 888) covalent geometry : bond 0.00288 ( 3152) covalent geometry : angle 0.52419 ( 4244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.337 Fit side-chains REVERT: A 81 LYS cc_start: 0.8482 (tttt) cc_final: 0.7557 (tppt) REVERT: A 98 PRO cc_start: 0.8513 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: A 111 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: B 68 LEU cc_start: 0.7778 (mp) cc_final: 0.7549 (mm) REVERT: B 81 LYS cc_start: 0.8473 (tttt) cc_final: 0.7533 (tppt) REVERT: B 98 PRO cc_start: 0.8508 (Cg_endo) cc_final: 0.8236 (Cg_exo) REVERT: B 111 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: C 68 LEU cc_start: 0.7790 (mp) cc_final: 0.7560 (mm) REVERT: C 81 LYS cc_start: 0.8467 (tttt) cc_final: 0.7526 (tppt) REVERT: C 98 PRO cc_start: 0.8500 (Cg_endo) cc_final: 0.8230 (Cg_exo) REVERT: C 111 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: D 81 LYS cc_start: 0.8482 (tttt) cc_final: 0.7550 (tppt) REVERT: D 98 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8228 (Cg_exo) REVERT: D 111 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6930 (tt0) outliers start: 8 outliers final: 0 residues processed: 50 average time/residue: 1.3237 time to fit residues: 67.9470 Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 111 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.180786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.167092 restraints weight = 2850.015| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.54 r_work: 0.3991 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3152 Z= 0.152 Angle : 0.583 6.807 4244 Z= 0.279 Chirality : 0.035 0.104 492 Planarity : 0.003 0.019 552 Dihedral : 3.109 8.792 452 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 21.52 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.40), residues: 432 helix: 2.37 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.71 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 118 PHE 0.009 0.001 PHE C 79 TYR 0.010 0.002 TYR A 16 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 296) hydrogen bonds : angle 3.15507 ( 888) covalent geometry : bond 0.00331 ( 3152) covalent geometry : angle 0.58335 ( 4244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.10 seconds wall clock time: 44 minutes 12.59 seconds (2652.59 seconds total)