Starting phenix.real_space_refine on Wed Jun 4 13:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7j_47678/06_2025/9e7j_47678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7j_47678/06_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_47678/06_2025/9e7j_47678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7j_47678/06_2025/9e7j_47678.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7j_47678/06_2025/9e7j_47678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7j_47678/06_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-5710/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: 3.11, per 1000 atoms: 1.00 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: 0.85 Conformation dependent library (CDL) restraints added in 426.6 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: 0.27 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: 1.00 Time building geometry restraints manager: 1.02 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: 0.03 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: 3.600 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.770 Find NCS groups from input model: 0.070 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- 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 : 0.294 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: 1.4106 time to fit residues: 69.4002 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 : 0.296 ------------------------------------------------------------------------------- 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 = 0.179018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164091 restraints weight = 2909.320| |-----------------------------------------------------------------------------| 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: 0.3780 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 63.695 452 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 3.46473 ( 888) covalent geometry : bond 0.00320 ( 3152) covalent geometry : angle 0.53473 ( 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 : 0.360 Fit side-chains REVERT: A 43 MET cc_start: 0.7239 (mtt) cc_final: 0.6946 (mtm) REVERT: A 81 LYS cc_start: 0.8514 (tttt) cc_final: 0.7690 (tppt) REVERT: B 43 MET cc_start: 0.7264 (mtt) cc_final: 0.6968 (mtm) REVERT: B 81 LYS cc_start: 0.8524 (tttt) cc_final: 0.7673 (tppt) REVERT: C 43 MET cc_start: 0.7264 (mtt) cc_final: 0.6968 (mtm) REVERT: C 81 LYS cc_start: 0.8520 (tttt) cc_final: 0.7671 (tppt) REVERT: D 43 MET cc_start: 0.7240 (mtt) cc_final: 0.6947 (mtm) REVERT: D 81 LYS cc_start: 0.8525 (tttt) cc_final: 0.7693 (tppt) outliers start: 8 outliers final: 0 residues processed: 46 average time/residue: 1.3824 time to fit residues: 65.2700 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 : 0.334 ------------------------------------------------------------------------------- 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: 0.5980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.174462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160654 restraints weight = 2989.660| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.53 r_work: 0.3917 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3152 Z= 0.166 Angle : 0.532 5.918 4244 Z= 0.270 Chirality : 0.036 0.110 492 Planarity : 0.003 0.024 552 Dihedral : 6.175 55.137 452 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 6.17 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: 2.24 (0.40), residues: 432 helix: 1.68 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.61 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 118 PHE 0.008 0.001 PHE C 79 TYR 0.011 0.002 TYR A 16 ARG 0.001 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 296) hydrogen bonds : angle 3.37923 ( 888) covalent geometry : bond 0.00362 ( 3152) covalent geometry : angle 0.53237 ( 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 : 0.344 Fit side-chains REVERT: A 43 MET cc_start: 0.7317 (mtt) cc_final: 0.6970 (mtm) REVERT: A 81 LYS cc_start: 0.8617 (tttt) cc_final: 0.7765 (tppt) REVERT: B 43 MET cc_start: 0.7316 (mtt) cc_final: 0.6976 (mtm) REVERT: B 68 LEU cc_start: 0.7969 (mp) cc_final: 0.7659 (mm) REVERT: B 81 LYS cc_start: 0.8589 (tttt) cc_final: 0.7704 (tppt) REVERT: C 43 MET cc_start: 0.7291 (mtt) cc_final: 0.6949 (mtm) REVERT: C 68 LEU cc_start: 0.7960 (mp) cc_final: 0.7644 (mm) REVERT: C 81 LYS cc_start: 0.8580 (tttt) cc_final: 0.7707 (tppt) REVERT: D 43 MET cc_start: 0.7326 (mtt) cc_final: 0.6978 (mtm) REVERT: D 81 LYS cc_start: 0.8611 (tttt) cc_final: 0.7751 (tppt) outliers start: 12 outliers final: 0 residues processed: 48 average time/residue: 1.5174 time to fit residues: 74.7013 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 : 0.376 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.172934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.159083 restraints weight = 3027.584| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.56 r_work: 0.3895 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3152 Z= 0.174 Angle : 0.550 6.193 4244 Z= 0.277 Chirality : 0.036 0.108 492 Planarity : 0.003 0.023 552 Dihedral : 5.392 45.030 452 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.53 % Allowed : 15.82 % 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: 2.33 (0.40), residues: 432 helix: 1.75 (0.27), residues: 372 sheet: None (None), residues: 0 loop : 0.51 (0.74), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 118 PHE 0.009 0.001 PHE B 79 TYR 0.011 0.002 TYR C 16 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05387 ( 296) hydrogen bonds : angle 3.38464 ( 888) covalent geometry : bond 0.00386 ( 3152) covalent geometry : angle 0.55009 ( 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 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.319 Fit side-chains REVERT: A 43 MET cc_start: 0.7308 (mtt) cc_final: 0.6888 (mtm) REVERT: A 81 LYS cc_start: 0.8634 (tttt) cc_final: 0.7758 (tppt) REVERT: B 43 MET cc_start: 0.7322 (mtt) cc_final: 0.6905 (mtm) REVERT: B 68 LEU cc_start: 0.7964 (mp) cc_final: 0.7672 (mm) REVERT: B 81 LYS cc_start: 0.8618 (tttt) cc_final: 0.7722 (tppt) REVERT: C 43 MET cc_start: 0.7309 (mtt) cc_final: 0.6892 (mtm) REVERT: C 68 LEU cc_start: 0.7942 (mp) cc_final: 0.7644 (mm) REVERT: C 81 LYS cc_start: 0.8611 (tttt) cc_final: 0.7728 (tppt) REVERT: D 43 MET cc_start: 0.7330 (mtt) cc_final: 0.6909 (mtm) REVERT: D 81 LYS cc_start: 0.8633 (tttt) cc_final: 0.7753 (tppt) outliers start: 8 outliers final: 0 residues processed: 46 average time/residue: 1.4319 time to fit residues: 67.6738 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 : 0.319 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.171564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157830 restraints weight = 2979.587| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.56 r_work: 0.3882 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3152 Z= 0.185 Angle : 0.572 6.602 4244 Z= 0.287 Chirality : 0.036 0.108 492 Planarity : 0.003 0.022 552 Dihedral : 4.561 32.511 452 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 6.99 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: 2.32 (0.40), residues: 432 helix: 1.82 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.06 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.001 PHE B 79 TYR 0.012 0.002 TYR B 16 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 296) hydrogen bonds : angle 3.44562 ( 888) covalent geometry : bond 0.00414 ( 3152) covalent geometry : angle 0.57197 ( 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 : 0.345 Fit side-chains REVERT: A 81 LYS cc_start: 0.8655 (tttt) cc_final: 0.7770 (tppt) REVERT: A 111 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: B 68 LEU cc_start: 0.7965 (mp) cc_final: 0.7698 (mm) REVERT: B 81 LYS cc_start: 0.8650 (tttt) cc_final: 0.7751 (tppt) REVERT: B 111 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6854 (tt0) REVERT: C 68 LEU cc_start: 0.7957 (mp) cc_final: 0.7683 (mm) REVERT: C 81 LYS cc_start: 0.8641 (tttt) cc_final: 0.7750 (tppt) REVERT: C 111 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: D 81 LYS cc_start: 0.8645 (tttt) cc_final: 0.7762 (tppt) REVERT: D 111 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6633 (tt0) outliers start: 6 outliers final: 0 residues processed: 50 average time/residue: 1.3223 time to fit residues: 67.9122 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.171688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157816 restraints weight = 3059.992| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.61 r_work: 0.3874 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3152 Z= 0.181 Angle : 0.572 6.713 4244 Z= 0.286 Chirality : 0.036 0.108 492 Planarity : 0.003 0.022 552 Dihedral : 3.937 21.598 452 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 : 2.53 % Allowed : 18.99 % 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: 2.41 (0.40), residues: 432 helix: 1.87 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.13 (0.74), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 118 PHE 0.009 0.001 PHE C 79 TYR 0.012 0.002 TYR D 16 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 296) hydrogen bonds : angle 3.43225 ( 888) covalent geometry : bond 0.00404 ( 3152) covalent geometry : angle 0.57248 ( 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 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.301 Fit side-chains REVERT: A 81 LYS cc_start: 0.8579 (tttt) cc_final: 0.7658 (tppt) REVERT: A 98 PRO cc_start: 0.8470 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: A 111 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: B 68 LEU cc_start: 0.7824 (mp) cc_final: 0.7560 (mm) REVERT: B 81 LYS cc_start: 0.8586 (tttt) cc_final: 0.7642 (tppt) REVERT: B 98 PRO cc_start: 0.8471 (Cg_endo) cc_final: 0.8207 (Cg_exo) REVERT: B 111 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: C 68 LEU cc_start: 0.7808 (mp) cc_final: 0.7541 (mm) REVERT: C 81 LYS cc_start: 0.8584 (tttt) cc_final: 0.7646 (tppt) REVERT: C 98 PRO cc_start: 0.8471 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: C 111 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: D 81 LYS cc_start: 0.8577 (tttt) cc_final: 0.7652 (tppt) REVERT: D 98 PRO cc_start: 0.8463 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: D 111 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6768 (tt0) outliers start: 8 outliers final: 0 residues processed: 56 average time/residue: 1.2821 time to fit residues: 73.9223 Evaluate side-chains 48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.172314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158590 restraints weight = 2991.244| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.57 r_work: 0.3885 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2478 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= 0.173 Angle : 0.567 6.533 4244 Z= 0.283 Chirality : 0.036 0.107 492 Planarity : 0.003 0.022 552 Dihedral : 3.584 14.143 452 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 19.62 % 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: 2.54 (0.40), residues: 432 helix: 1.95 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.28 (0.75), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.009 0.001 PHE C 79 TYR 0.011 0.002 TYR C 16 ARG 0.001 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05334 ( 296) hydrogen bonds : angle 3.38617 ( 888) covalent geometry : bond 0.00382 ( 3152) covalent geometry : angle 0.56696 ( 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 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.314 Fit side-chains REVERT: A 81 LYS cc_start: 0.8559 (tttt) cc_final: 0.7644 (tppt) REVERT: A 98 PRO cc_start: 0.8477 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: A 111 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: B 68 LEU cc_start: 0.7807 (mp) cc_final: 0.7559 (mm) REVERT: B 81 LYS cc_start: 0.8578 (tttt) cc_final: 0.7627 (tppt) REVERT: B 98 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8207 (Cg_exo) REVERT: B 111 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: C 68 LEU cc_start: 0.7799 (mp) cc_final: 0.7547 (mm) REVERT: C 81 LYS cc_start: 0.8573 (tttt) cc_final: 0.7626 (tppt) REVERT: C 98 PRO cc_start: 0.8480 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: C 111 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: D 81 LYS cc_start: 0.8556 (tttt) cc_final: 0.7637 (tppt) REVERT: D 98 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8208 (Cg_exo) REVERT: D 111 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6762 (tt0) outliers start: 6 outliers final: 0 residues processed: 50 average time/residue: 1.4057 time to fit residues: 72.0632 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 : 0.313 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.0060 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.176618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162785 restraints weight = 2986.829| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.59 r_work: 0.3954 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2679 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= 0.139 Angle : 0.509 5.914 4244 Z= 0.254 Chirality : 0.034 0.106 492 Planarity : 0.003 0.021 552 Dihedral : 3.252 9.095 452 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.90 % Allowed : 19.62 % 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: 3.04 (0.40), residues: 432 helix: 2.30 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.39 (0.78), 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 0.009 0.001 TYR D 16 ARG 0.000 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 296) hydrogen bonds : angle 3.14647 ( 888) covalent geometry : bond 0.00286 ( 3152) covalent geometry : angle 0.50882 ( 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 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.265 Fit side-chains REVERT: A 81 LYS cc_start: 0.8550 (tttt) cc_final: 0.7669 (tppt) REVERT: A 98 PRO cc_start: 0.8470 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: B 68 LEU cc_start: 0.7907 (mp) cc_final: 0.7682 (mm) REVERT: B 81 LYS cc_start: 0.8558 (tttt) cc_final: 0.7641 (tppt) REVERT: B 98 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.8193 (Cg_exo) REVERT: C 68 LEU cc_start: 0.7896 (mp) cc_final: 0.7662 (mm) REVERT: C 81 LYS cc_start: 0.8554 (tttt) cc_final: 0.7640 (tppt) REVERT: C 98 PRO cc_start: 0.8459 (Cg_endo) cc_final: 0.8189 (Cg_exo) REVERT: D 81 LYS cc_start: 0.8551 (tttt) cc_final: 0.7667 (tppt) REVERT: D 98 PRO cc_start: 0.8468 (Cg_endo) cc_final: 0.8199 (Cg_exo) outliers start: 6 outliers final: 0 residues processed: 54 average time/residue: 1.1955 time to fit residues: 66.4739 Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.0020 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.1924 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.187077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172773 restraints weight = 2918.712| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 1.70 r_work: 0.4056 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3152 Z= 0.112 Angle : 0.473 5.371 4244 Z= 0.233 Chirality : 0.033 0.104 492 Planarity : 0.002 0.020 552 Dihedral : 2.962 8.152 452 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 21.52 % 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: 4.03 (0.40), residues: 432 helix: 2.87 (0.26), residues: 364 sheet: None (None), residues: 0 loop : 1.50 (0.89), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 36 PHE 0.005 0.001 PHE C 79 TYR 0.005 0.001 TYR D 16 ARG 0.001 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 296) hydrogen bonds : angle 2.82711 ( 888) covalent geometry : bond 0.00206 ( 3152) covalent geometry : angle 0.47255 ( 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 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.295 Fit side-chains REVERT: A 43 MET cc_start: 0.7042 (mtt) cc_final: 0.6654 (mtm) REVERT: A 81 LYS cc_start: 0.8372 (tttt) cc_final: 0.7459 (tppt) REVERT: A 98 PRO cc_start: 0.8502 (Cg_endo) cc_final: 0.8234 (Cg_exo) REVERT: B 43 MET cc_start: 0.7055 (mtt) cc_final: 0.6669 (mtm) REVERT: B 68 LEU cc_start: 0.7700 (mp) cc_final: 0.7476 (mm) REVERT: B 81 LYS cc_start: 0.8381 (tttt) cc_final: 0.7452 (tppt) REVERT: B 98 PRO cc_start: 0.8519 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: C 43 MET cc_start: 0.7069 (mtt) cc_final: 0.6683 (mtm) REVERT: C 68 LEU cc_start: 0.7694 (mp) cc_final: 0.7471 (mm) REVERT: C 81 LYS cc_start: 0.8384 (tttt) cc_final: 0.7458 (tppt) REVERT: C 98 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.8237 (Cg_exo) REVERT: D 43 MET cc_start: 0.7039 (mtt) cc_final: 0.6653 (mtm) REVERT: D 81 LYS cc_start: 0.8385 (tttt) cc_final: 0.7470 (tppt) REVERT: D 98 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8227 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 1.3293 time to fit residues: 62.8608 Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.172803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.159301 restraints weight = 2969.714| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.62 r_work: 0.3895 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3152 Z= 0.175 Angle : 0.583 6.463 4244 Z= 0.290 Chirality : 0.036 0.108 492 Planarity : 0.003 0.019 552 Dihedral : 3.192 9.165 452 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.27 % Allowed : 21.52 % Favored : 77.22 % 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: 3.17 (0.40), residues: 432 helix: 2.38 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.45 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 118 PHE 0.011 0.001 PHE C 79 TYR 0.012 0.002 TYR A 16 ARG 0.001 0.001 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 296) hydrogen bonds : angle 3.27862 ( 888) covalent geometry : bond 0.00390 ( 3152) covalent geometry : angle 0.58326 ( 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: 4 poor density : 46 time to evaluate : 0.344 Fit side-chains REVERT: A 81 LYS cc_start: 0.8546 (tttt) cc_final: 0.7625 (tppt) REVERT: A 98 PRO cc_start: 0.8526 (Cg_endo) cc_final: 0.8247 (Cg_exo) REVERT: B 68 LEU cc_start: 0.7774 (mp) cc_final: 0.7542 (mm) REVERT: B 81 LYS cc_start: 0.8535 (tttt) cc_final: 0.7592 (tppt) REVERT: B 98 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: C 68 LEU cc_start: 0.7754 (mp) cc_final: 0.7518 (mm) REVERT: C 81 LYS cc_start: 0.8545 (tttt) cc_final: 0.7608 (tppt) REVERT: C 98 PRO cc_start: 0.8524 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: D 81 LYS cc_start: 0.8547 (tttt) cc_final: 0.7620 (tppt) REVERT: D 98 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.8236 (Cg_exo) outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 1.2661 time to fit residues: 62.5069 Evaluate side-chains 46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160473 restraints weight = 2954.837| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.55 r_work: 0.3908 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3152 Z= 0.170 Angle : 0.579 6.816 4244 Z= 0.288 Chirality : 0.036 0.108 492 Planarity : 0.003 0.019 552 Dihedral : 3.264 9.181 452 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.63 % Allowed : 22.15 % Favored : 77.22 % 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: 2.97 (0.40), residues: 432 helix: 2.24 (0.27), residues: 368 sheet: None (None), residues: 0 loop : 0.42 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 118 PHE 0.010 0.001 PHE C 79 TYR 0.011 0.002 TYR B 16 ARG 0.001 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 296) hydrogen bonds : angle 3.29901 ( 888) covalent geometry : bond 0.00377 ( 3152) covalent geometry : angle 0.57896 ( 4244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2627.99 seconds wall clock time: 46 minutes 2.38 seconds (2762.38 seconds total)