Starting phenix.real_space_refine on Wed Mar 5 14:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihu_35459/03_2025/8ihu_35459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihu_35459/03_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_35459/03_2025/8ihu_35459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihu_35459/03_2025/8ihu_35459.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihu_35459/03_2025/8ihu_35459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihu_35459/03_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-5624/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: 1.10, per 1000 atoms: 0.72 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: 1.47 Conformation dependent library (CDL) restraints added in 158.6 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: 0.24 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: 0.30 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: 2.760 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.110 Find NCS groups from input model: 0.030 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- 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 : 0.166 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: 1.0656 time to fit residues: 40.1700 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 : 0.171 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.114281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.101877 restraints weight = 2133.487| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.11 r_work: 0.3407 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1530 Z= 0.238 Angle : 0.697 7.559 2058 Z= 0.359 Chirality : 0.048 0.137 249 Planarity : 0.003 0.013 276 Dihedral : 5.136 20.815 222 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % 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 : -3.88 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.171 Fit side-chains REVERT: A 122 LYS cc_start: 0.8095 (mttp) cc_final: 0.7780 (mtpp) REVERT: A 151 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7822 (mt) REVERT: C 151 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7074 (mt) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 1.1304 time to fit residues: 37.9803 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 : 0.172 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.108564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096535 restraints weight = 2107.197| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.15 r_work: 0.3322 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1530 Z= 0.266 Angle : 0.673 5.394 2058 Z= 0.353 Chirality : 0.048 0.135 249 Planarity : 0.003 0.019 276 Dihedral : 5.271 21.185 222 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.29 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: -4.90 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.154 Fit side-chains REVERT: A 122 LYS cc_start: 0.8193 (mttp) cc_final: 0.7857 (mtpp) REVERT: A 151 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7680 (mt) REVERT: B 122 LYS cc_start: 0.8259 (mttp) cc_final: 0.7836 (mtpp) REVERT: B 151 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7553 (mt) outliers start: 6 outliers final: 1 residues processed: 31 average time/residue: 1.1972 time to fit residues: 37.7533 Evaluate side-chains 30 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.113717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101179 restraints weight = 2085.947| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.17 r_work: 0.3396 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3753 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= 0.167 Angle : 0.603 4.673 2058 Z= 0.320 Chirality : 0.048 0.133 249 Planarity : 0.002 0.016 276 Dihedral : 4.650 18.975 222 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 2.42 % Allowed : 16.36 % Favored : 81.21 % 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: -4.55 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 110 ARG 0.003 0.000 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 35 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.184 Fit side-chains REVERT: A 122 LYS cc_start: 0.8214 (mttp) cc_final: 0.7868 (mtpp) REVERT: A 151 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7472 (mt) REVERT: B 122 LYS cc_start: 0.8245 (mttp) cc_final: 0.7848 (mtpp) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 1.1561 time to fit residues: 36.5252 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095434 restraints weight = 2074.271| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.10 r_work: 0.3302 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 1530 Z= 0.384 Angle : 0.733 5.683 2058 Z= 0.385 Chirality : 0.051 0.140 249 Planarity : 0.004 0.035 276 Dihedral : 5.535 23.035 222 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.90 % Favored : 78.10 % Rotamer: Outliers : 3.64 % Allowed : 15.15 % Favored : 81.21 % 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: -4.65 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 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 32 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.178 Fit side-chains REVERT: A 122 LYS cc_start: 0.8244 (mttp) cc_final: 0.7837 (mtpp) REVERT: A 151 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7852 (mt) REVERT: B 122 LYS cc_start: 0.8338 (mttp) cc_final: 0.7909 (mtpp) outliers start: 6 outliers final: 1 residues processed: 27 average time/residue: 1.1240 time to fit residues: 30.9777 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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: 4.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.112961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100405 restraints weight = 2101.520| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.17 r_work: 0.3381 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3998 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= 0.193 Angle : 0.609 4.864 2058 Z= 0.321 Chirality : 0.048 0.137 249 Planarity : 0.003 0.021 276 Dihedral : 4.852 19.932 222 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % 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: -4.45 (0.47), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 110 ARG 0.004 0.000 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 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.163 Fit side-chains REVERT: A 122 LYS cc_start: 0.8265 (mttp) cc_final: 0.7851 (mtpp) REVERT: A 151 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7416 (mt) REVERT: B 122 LYS cc_start: 0.8284 (mttp) cc_final: 0.7864 (mtpp) REVERT: B 151 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7571 (mt) outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 1.1458 time to fit residues: 31.5474 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 : 0.176 ------------------------------------------------------------------------------- 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 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 2 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.120539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107363 restraints weight = 2035.783| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.21 r_work: 0.3490 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4256 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= 0.127 Angle : 0.559 4.803 2058 Z= 0.296 Chirality : 0.048 0.131 249 Planarity : 0.002 0.018 276 Dihedral : 4.116 16.510 222 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: -4.32 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 120 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 31 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.175 Fit side-chains REVERT: A 122 LYS cc_start: 0.8247 (mttp) cc_final: 0.7866 (mtpp) REVERT: A 151 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6816 (tt) REVERT: B 122 LYS cc_start: 0.8285 (mttp) cc_final: 0.7908 (mtpp) REVERT: B 151 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7275 (mt) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 1.1529 time to fit residues: 31.7483 Evaluate side-chains 30 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095725 restraints weight = 2293.915| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.26 r_work: 0.3332 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4078 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= 0.334 Angle : 0.710 6.437 2058 Z= 0.369 Chirality : 0.051 0.141 249 Planarity : 0.004 0.030 276 Dihedral : 5.198 20.783 222 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 1.82 % Allowed : 19.39 % 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: -4.42 (0.48), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.004 0.001 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: 3 poor density : 25 time to evaluate : 0.171 Fit side-chains REVERT: A 122 LYS cc_start: 0.8309 (mttp) cc_final: 0.7909 (mtpp) REVERT: A 131 ASN cc_start: 0.8611 (t0) cc_final: 0.8352 (t0) REVERT: A 151 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7628 (mt) REVERT: B 122 LYS cc_start: 0.8299 (mttp) cc_final: 0.7878 (mtpp) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.1201 time to fit residues: 29.7133 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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: 3.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.109815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097243 restraints weight = 2313.548| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.27 r_work: 0.3370 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1530 Z= 0.244 Angle : 0.664 6.286 2058 Z= 0.346 Chirality : 0.049 0.176 249 Planarity : 0.003 0.026 276 Dihedral : 4.987 18.948 222 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.82 % Allowed : 20.00 % Favored : 78.18 % 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 (0.48), 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 0.001 0.001 HIS C 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 27 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.169 Fit side-chains REVERT: A 122 LYS cc_start: 0.8286 (mttp) cc_final: 0.7922 (mtpp) REVERT: A 151 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7372 (mt) REVERT: B 122 LYS cc_start: 0.8228 (mttp) cc_final: 0.7810 (mtpp) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 1.1198 time to fit residues: 28.5603 Evaluate side-chains 24 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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: 0.8980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 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 = 0.3686 r_free = 0.3686 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101908 restraints weight = 2103.886| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.18 r_work: 0.3427 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1530 Z= 0.178 Angle : 0.620 6.512 2058 Z= 0.321 Chirality : 0.048 0.146 249 Planarity : 0.003 0.018 276 Dihedral : 4.602 16.503 222 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.18 % 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: -4.32 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.172 Fit side-chains REVERT: A 122 LYS cc_start: 0.8288 (mttp) cc_final: 0.7937 (mtpp) REVERT: A 151 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7035 (mt) REVERT: B 122 LYS cc_start: 0.8251 (mttp) cc_final: 0.7796 (mtpp) REVERT: C 122 LYS cc_start: 0.8264 (mttp) cc_final: 0.7900 (mtpm) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 1.1416 time to fit residues: 36.0823 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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: 0.6980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 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 = 0.3691 r_free = 0.3691 target = 0.114842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102026 restraints weight = 2153.001| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.22 r_work: 0.3430 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1530 Z= 0.183 Angle : 0.639 6.298 2058 Z= 0.335 Chirality : 0.049 0.160 249 Planarity : 0.003 0.019 276 Dihedral : 4.552 15.897 222 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 2.42 % Allowed : 19.39 % Favored : 78.18 % 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 : -3.26 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.07 seconds wall clock time: 31 minutes 33.22 seconds (1893.22 seconds total)