Starting phenix.real_space_refine on Mon Feb 10 19:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihu_35459/02_2025/8ihu_35459.cif" } resolution = 2.97 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= 0.002 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 6 5.16 5 C 912 2.51 5 N 279 2.21 5 O 330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1527 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Restraints were copied for chains: C, B Time building chain proxies: 1.04, per 1000 atoms: 0.68 Number of scatterers: 1527 At special positions: 0 Unit cell: (82.32, 68.88, 36.96, 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 6 16.00 O 330 8.00 N 279 7.00 C 912 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: 1.49 Conformation dependent library (CDL) restraints added in 199.2 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 366 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.509A pdb=" N SER A 98 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 98 " --> pdb=" O ILE C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.379A pdb=" N VAL A 103 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU B 106 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 105 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 103 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU C 106 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 105 " --> pdb=" O LEU C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.642A pdb=" N ILE A 112 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 112 " --> pdb=" O ILE C 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.539A pdb=" N ASN A 139 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.651A pdb=" N ARG A 143 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 143 " --> pdb=" O LEU C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 9 hydrogen bonds defined for protein. 27 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: 0.31 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 564 1.34 - 1.46: 144 1.46 - 1.57: 816 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 1530 Sorted by residual: bond pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.09e-01 bond pdb=" CG GLU C 100 " pdb=" CD GLU C 100 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.68e-01 bond pdb=" CG GLU B 100 " pdb=" CD GLU B 100 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.60e-01 bond pdb=" CB ASP B 90 " pdb=" CG ASP B 90 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.78e-01 bond pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.66e-01 ... (remaining 1525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 1883 1.11 - 2.22: 137 2.22 - 3.32: 25 3.32 - 4.43: 4 4.43 - 5.54: 9 Bond angle restraints: 2058 Sorted by residual: angle pdb=" N ILE C 149 " pdb=" CA ILE C 149 " pdb=" C ILE C 149 " ideal model delta sigma weight residual 109.34 114.88 -5.54 2.08e+00 2.31e-01 7.09e+00 angle pdb=" N ILE B 149 " pdb=" CA ILE B 149 " pdb=" C ILE B 149 " ideal model delta sigma weight residual 109.34 114.87 -5.53 2.08e+00 2.31e-01 7.08e+00 angle pdb=" N ILE A 149 " pdb=" CA ILE A 149 " pdb=" C ILE A 149 " ideal model delta sigma weight residual 109.34 114.86 -5.52 2.08e+00 2.31e-01 7.04e+00 angle pdb=" CA GLU C 100 " pdb=" CB GLU C 100 " pdb=" CG GLU C 100 " ideal model delta sigma weight residual 114.10 110.52 3.58 2.00e+00 2.50e-01 3.21e+00 angle pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " pdb=" CG GLU B 100 " ideal model delta sigma weight residual 114.10 110.53 3.57 2.00e+00 2.50e-01 3.18e+00 ... (remaining 2053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 780 11.41 - 22.81: 93 22.81 - 34.22: 36 34.22 - 45.62: 3 45.62 - 57.03: 6 Dihedral angle restraints: 918 sinusoidal: 339 harmonic: 579 Sorted by residual: dihedral pdb=" CA GLU A 100 " pdb=" C GLU A 100 " pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU C 100 " pdb=" C GLU C 100 " pdb=" N ASP C 101 " pdb=" CA ASP C 101 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU B 100 " pdb=" C GLU B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 145 0.028 - 0.056: 44 0.056 - 0.084: 22 0.084 - 0.112: 32 0.112 - 0.140: 6 Chirality restraints: 249 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 246 not shown) Planarity restraints: 276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 84 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C LEU B 84 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU B 84 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 85 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 84 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU A 84 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 84 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 85 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 84 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C LEU C 84 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU C 84 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG C 85 " 0.007 2.00e-02 2.50e+03 ... (remaining 273 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 20 2.61 - 3.18: 1305 3.18 - 3.76: 2150 3.76 - 4.33: 2804 4.33 - 4.90: 5255 Nonbonded interactions: 11534 Sorted by model distance: nonbonded pdb=" NE2 GLN A 153 " pdb=" O HIS B 110 " model vdw 2.039 3.120 nonbonded pdb=" NE2 GLN B 153 " pdb=" O HIS C 110 " model vdw 2.361 3.120 nonbonded pdb=" N LEU B 117 " pdb=" O THR C 116 " model vdw 2.417 3.120 nonbonded pdb=" NE2 GLN A 153 " pdb=" O CYS C 111 " model vdw 2.434 3.120 nonbonded pdb=" NH1 ARG A 85 " pdb=" OD2 ASP A 101 " model vdw 2.510 3.120 ... (remaining 11529 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.630 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.005 0.022 1530 Z= 0.321 Angle : 0.724 5.538 2058 Z= 0.392 Chirality : 0.050 0.140 249 Planarity : 0.003 0.013 276 Dihedral : 12.543 57.030 552 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: -5.66 (0.36), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 110 ARG 0.003 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.159 Fit side-chains REVERT: A 132 GLU cc_start: 0.8009 (tt0) cc_final: 0.7566 (tm-30) REVERT: B 122 LYS cc_start: 0.7779 (mttp) cc_final: 0.7520 (mtpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 1.0367 time to fit residues: 39.0726 Evaluate side-chains 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 120 HIS C 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100370 restraints weight = 2137.073| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.22 r_work: 0.3400 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1530 Z= 0.240 Angle : 0.699 7.317 2058 Z= 0.361 Chirality : 0.048 0.134 249 Planarity : 0.003 0.013 276 Dihedral : 5.213 21.290 222 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 1.21 % Allowed : 15.15 % Favored : 83.64 % 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: -5.09 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 110 ARG 0.003 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.175 Fit side-chains REVERT: A 122 LYS cc_start: 0.8119 (mttp) cc_final: 0.7816 (mtpp) REVERT: A 151 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 151 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7046 (mt) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 1.0914 time to fit residues: 35.6150 Evaluate side-chains 29 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 15 optimal weight: 0.0470 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.117810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105113 restraints weight = 2061.663| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.16 r_work: 0.3456 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1530 Z= 0.136 Angle : 0.559 4.735 2058 Z= 0.296 Chirality : 0.047 0.129 249 Planarity : 0.002 0.015 276 Dihedral : 4.332 17.510 222 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 2.42 % Allowed : 16.97 % Favored : 80.61 % 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: -4.68 (0.44), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.34), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 110 ARG 0.003 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.183 Fit side-chains REVERT: A 122 LYS cc_start: 0.8130 (mttp) cc_final: 0.7814 (mtpp) REVERT: A 151 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7232 (mt) REVERT: B 122 LYS cc_start: 0.8217 (mttp) cc_final: 0.7835 (mtpp) REVERT: B 151 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7483 (mt) outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 1.0203 time to fit residues: 37.4773 Evaluate side-chains 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.104208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092356 restraints weight = 2325.039| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.19 r_work: 0.3295 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 1530 Z= 0.319 Angle : 0.713 5.323 2058 Z= 0.368 Chirality : 0.050 0.139 249 Planarity : 0.003 0.028 276 Dihedral : 5.343 21.755 222 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.48 % Favored : 79.52 % Rotamer: Outliers : 3.64 % Allowed : 15.76 % Favored : 80.61 % 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: -4.67 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 110 ARG 0.003 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.162 Fit side-chains REVERT: A 122 LYS cc_start: 0.8187 (mttp) cc_final: 0.7775 (mtpp) REVERT: A 151 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7824 (mt) REVERT: B 122 LYS cc_start: 0.8253 (mttp) cc_final: 0.7786 (mtpp) REVERT: C 85 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6534 (ttt180) outliers start: 6 outliers final: 0 residues processed: 29 average time/residue: 1.2053 time to fit residues: 35.5995 Evaluate side-chains 27 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.111268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.099356 restraints weight = 2077.886| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.11 r_work: 0.3390 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1530 Z= 0.233 Angle : 0.641 5.069 2058 Z= 0.335 Chirality : 0.049 0.138 249 Planarity : 0.003 0.024 276 Dihedral : 5.002 19.163 222 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.85 % Allowed : 14.55 % Favored : 80.61 % 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: -4.52 (0.47), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 110 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.170 Fit side-chains REVERT: A 122 LYS cc_start: 0.8260 (mttp) cc_final: 0.7834 (mtpp) REVERT: A 151 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7365 (mt) REVERT: B 122 LYS cc_start: 0.8294 (mttp) cc_final: 0.7842 (mtpp) REVERT: B 151 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7524 (mt) REVERT: C 85 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6726 (ttt180) outliers start: 8 outliers final: 1 residues processed: 30 average time/residue: 1.1708 time to fit residues: 35.9023 Evaluate side-chains 27 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098558 restraints weight = 2306.481| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.29 r_work: 0.3380 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1530 Z= 0.210 Angle : 0.626 4.691 2058 Z= 0.328 Chirality : 0.049 0.136 249 Planarity : 0.003 0.021 276 Dihedral : 4.766 17.939 222 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % Rotamer: Outliers : 3.03 % Allowed : 16.36 % Favored : 80.61 % 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: -4.43 (0.48), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 110 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.177 Fit side-chains REVERT: A 122 LYS cc_start: 0.8288 (mttp) cc_final: 0.7844 (mtpp) REVERT: A 151 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7449 (mt) REVERT: B 122 LYS cc_start: 0.8285 (mttp) cc_final: 0.7825 (mtpp) REVERT: C 85 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6640 (ttt180) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 1.2115 time to fit residues: 30.8719 Evaluate side-chains 26 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.0980 chunk 18 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.115802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102954 restraints weight = 2257.779| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.29 r_work: 0.3444 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1530 Z= 0.143 Angle : 0.591 4.807 2058 Z= 0.312 Chirality : 0.048 0.150 249 Planarity : 0.002 0.017 276 Dihedral : 4.277 15.536 222 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.03 % Allowed : 17.58 % Favored : 79.39 % 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: -4.31 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 110 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.171 Fit side-chains REVERT: A 122 LYS cc_start: 0.8283 (mttp) cc_final: 0.7866 (mtpp) REVERT: A 151 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6969 (mt) REVERT: B 122 LYS cc_start: 0.8290 (mttp) cc_final: 0.7880 (mtpp) REVERT: C 85 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6803 (ttt180) outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 1.2017 time to fit residues: 36.7178 Evaluate side-chains 27 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.108157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096026 restraints weight = 2302.209| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.27 r_work: 0.3343 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1530 Z= 0.310 Angle : 0.715 7.923 2058 Z= 0.370 Chirality : 0.051 0.174 249 Planarity : 0.004 0.031 276 Dihedral : 5.106 19.247 222 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % Rotamer: Outliers : 3.64 % Allowed : 16.36 % Favored : 80.00 % 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: -4.38 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.169 Fit side-chains REVERT: A 122 LYS cc_start: 0.8277 (mttp) cc_final: 0.7898 (mtpp) REVERT: A 131 ASN cc_start: 0.8618 (t0) cc_final: 0.8371 (t0) REVERT: A 151 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7470 (mt) REVERT: B 122 LYS cc_start: 0.8253 (mttp) cc_final: 0.7839 (mtpp) REVERT: C 85 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6553 (ttt180) outliers start: 6 outliers final: 1 residues processed: 25 average time/residue: 1.2777 time to fit residues: 32.5222 Evaluate side-chains 24 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 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 = 0.3690 r_free = 0.3690 target = 0.114924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102300 restraints weight = 2102.802| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.17 r_work: 0.3420 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1530 Z= 0.173 Angle : 0.633 7.830 2058 Z= 0.327 Chirality : 0.049 0.171 249 Planarity : 0.003 0.018 276 Dihedral : 4.556 16.081 222 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % Favored : 78.79 % 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: -4.29 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 110 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.133 Fit side-chains REVERT: A 122 LYS cc_start: 0.8292 (mttp) cc_final: 0.7919 (mtpp) REVERT: A 132 GLU cc_start: 0.8630 (tt0) cc_final: 0.8023 (tm-30) REVERT: A 151 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7142 (tt) REVERT: B 122 LYS cc_start: 0.8286 (mttp) cc_final: 0.7843 (mtpp) REVERT: C 85 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6843 (ttt180) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 1.1939 time to fit residues: 35.1960 Evaluate side-chains 27 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102337 restraints weight = 2250.284| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.28 r_work: 0.3440 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1530 Z= 0.165 Angle : 0.615 7.824 2058 Z= 0.317 Chirality : 0.049 0.159 249 Planarity : 0.003 0.018 276 Dihedral : 4.377 14.787 222 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % Favored : 78.79 % 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: -4.28 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 110 ARG 0.004 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.166 Fit side-chains REVERT: A 122 LYS cc_start: 0.8348 (mttp) cc_final: 0.7929 (mtpp) REVERT: A 132 GLU cc_start: 0.8632 (tt0) cc_final: 0.8028 (tm-30) REVERT: A 151 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6971 (tt) REVERT: B 122 LYS cc_start: 0.8243 (mttp) cc_final: 0.7803 (mtpp) REVERT: C 85 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6884 (ttt180) REVERT: C 122 LYS cc_start: 0.8303 (mttp) cc_final: 0.7911 (mtpm) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 1.1954 time to fit residues: 37.6978 Evaluate side-chains 29 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099578 restraints weight = 2324.540| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.30 r_work: 0.3401 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1530 Z= 0.213 Angle : 0.654 7.444 2058 Z= 0.341 Chirality : 0.049 0.147 249 Planarity : 0.003 0.019 276 Dihedral : 4.585 16.058 222 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % Rotamer: Outliers : 2.42 % Allowed : 18.79 % Favored : 78.79 % 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: -4.28 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 110 ARG 0.004 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.47 seconds wall clock time: 31 minutes 28.19 seconds (1888.19 seconds total)