Starting phenix.real_space_refine on Fri Aug 22 12:38:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihu_35459/08_2025/8ihu_35459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihu_35459/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ihu_35459/08_2025/8ihu_35459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihu_35459/08_2025/8ihu_35459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihu_35459/08_2025/8ihu_35459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihu_35459/08_2025/8ihu_35459.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C Time building chain proxies: 0.43, per 1000 atoms: 0.28 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: 0.34 Conformation dependent library (CDL) restraints added in 130.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.09 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: 0.23 Time building geometry restraints manager: 0.40 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.730 Find NCS groups from input model: 0.020 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- 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= 0.211 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG A 85 HIS 0.005 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 1530) covalent geometry : angle 0.72388 ( 2058) hydrogen bonds : bond 0.29947 ( 9) hydrogen bonds : angle 9.79299 ( 27) *********************** 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 : 0.057 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: 0.5415 time to fit residues: 20.3809 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 : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 110 HIS C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102133 restraints weight = 2104.461| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.21 r_work: 0.3421 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2717 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= 0.136 Angle : 0.675 7.352 2058 Z= 0.347 Chirality : 0.048 0.130 249 Planarity : 0.003 0.013 276 Dihedral : 5.042 20.854 222 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.06 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1530) covalent geometry : angle 0.67539 ( 2058) hydrogen bonds : bond 0.03067 ( 9) hydrogen bonds : angle 5.36584 ( 27) *********************** 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 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.062 Fit side-chains REVERT: A 151 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7787 (mt) REVERT: B 151 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7514 (mt) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.5391 time to fit residues: 18.6453 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 : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096916 restraints weight = 2156.176| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.18 r_work: 0.3325 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3563 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= 0.161 Angle : 0.664 5.339 2058 Z= 0.350 Chirality : 0.048 0.142 249 Planarity : 0.003 0.016 276 Dihedral : 5.235 20.814 222 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.85 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 143 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 1530) covalent geometry : angle 0.66396 ( 2058) hydrogen bonds : bond 0.03250 ( 9) hydrogen bonds : angle 5.45235 ( 27) *********************** 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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.064 Fit side-chains REVERT: A 122 LYS cc_start: 0.8198 (mttp) cc_final: 0.7864 (mtpp) REVERT: A 151 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7600 (mt) REVERT: B 122 LYS cc_start: 0.8265 (mttp) cc_final: 0.7836 (mtpp) REVERT: B 151 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7650 (mt) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.6104 time to fit residues: 19.2119 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 : 0.062 ------------------------------------------------------------------------------- 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 2 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 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 = 0.3648 r_free = 0.3648 target = 0.111395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098905 restraints weight = 2121.364| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.19 r_work: 0.3365 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1530 Z= 0.139 Angle : 0.632 4.784 2058 Z= 0.334 Chirality : 0.048 0.136 249 Planarity : 0.003 0.017 276 Dihedral : 4.924 20.006 222 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 1530) covalent geometry : angle 0.63212 ( 2058) hydrogen bonds : bond 0.02631 ( 9) hydrogen bonds : angle 5.25285 ( 27) *********************** 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 : 0.059 Fit side-chains REVERT: A 122 LYS cc_start: 0.8226 (mttp) cc_final: 0.7871 (mtpp) REVERT: A 131 ASN cc_start: 0.8631 (t0) cc_final: 0.8395 (t0) REVERT: A 151 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7437 (mt) REVERT: B 122 LYS cc_start: 0.8287 (mttp) cc_final: 0.7868 (mtpp) REVERT: B 151 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7631 (mt) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 0.5975 time to fit residues: 18.8155 Evaluate side-chains 28 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.116028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103134 restraints weight = 2255.541| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.28 r_work: 0.3439 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1530 Z= 0.096 Angle : 0.571 4.486 2058 Z= 0.300 Chirality : 0.047 0.130 249 Planarity : 0.002 0.016 276 Dihedral : 4.281 17.316 222 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.48), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 HIS 0.001 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 1530) covalent geometry : angle 0.57050 ( 2058) hydrogen bonds : bond 0.01986 ( 9) hydrogen bonds : angle 4.75454 ( 27) *********************** 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 34 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.060 Fit side-chains REVERT: A 122 LYS cc_start: 0.8243 (mttp) cc_final: 0.7870 (mtpp) REVERT: A 151 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7196 (mt) REVERT: B 122 LYS cc_start: 0.8283 (mttp) cc_final: 0.7881 (mtpp) REVERT: B 126 LEU cc_start: 0.8536 (mt) cc_final: 0.8331 (mp) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 0.5717 time to fit residues: 16.8502 Evaluate side-chains 30 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.112263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099787 restraints weight = 2243.716| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.24 r_work: 0.3387 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1530 Z= 0.135 Angle : 0.607 4.708 2058 Z= 0.318 Chirality : 0.048 0.136 249 Planarity : 0.003 0.018 276 Dihedral : 4.664 17.986 222 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.48), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 143 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1530) covalent geometry : angle 0.60669 ( 2058) hydrogen bonds : bond 0.02482 ( 9) hydrogen bonds : angle 5.10145 ( 27) *********************** 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 30 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.116 Fit side-chains REVERT: A 122 LYS cc_start: 0.8306 (mttp) cc_final: 0.7903 (mtpp) REVERT: A 151 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7274 (mt) REVERT: B 122 LYS cc_start: 0.8298 (mttp) cc_final: 0.7891 (mtpp) REVERT: B 151 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7462 (mt) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 0.5870 time to fit residues: 15.5138 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 : 0.037 ------------------------------------------------------------------------------- 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 3 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.106893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094891 restraints weight = 2102.097| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.12 r_work: 0.3285 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 1530 Z= 0.277 Angle : 0.775 5.961 2058 Z= 0.405 Chirality : 0.052 0.149 249 Planarity : 0.004 0.046 276 Dihedral : 5.667 22.792 222 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 2.42 % Allowed : 17.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.47 (0.48), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 1530) covalent geometry : angle 0.77489 ( 2058) hydrogen bonds : bond 0.03592 ( 9) hydrogen bonds : angle 5.40172 ( 27) *********************** 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 25 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.063 Fit side-chains REVERT: A 131 ASN cc_start: 0.8680 (t0) cc_final: 0.8438 (t0) REVERT: A 151 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 122 LYS cc_start: 0.8291 (mttp) cc_final: 0.7928 (mtpp) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.5784 time to fit residues: 12.9531 Evaluate side-chains 23 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 2 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.110760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098127 restraints weight = 2155.547| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.21 r_work: 0.3336 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1530 Z= 0.169 Angle : 0.661 5.134 2058 Z= 0.348 Chirality : 0.049 0.146 249 Planarity : 0.003 0.028 276 Dihedral : 5.179 19.763 222 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 143 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 1530) covalent geometry : angle 0.66092 ( 2058) hydrogen bonds : bond 0.02889 ( 9) hydrogen bonds : angle 5.24780 ( 27) *********************** 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 26 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.062 Fit side-chains REVERT: A 131 ASN cc_start: 0.8622 (t0) cc_final: 0.8369 (t0) REVERT: A 151 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (mt) REVERT: B 122 LYS cc_start: 0.8326 (mttp) cc_final: 0.7974 (mtpp) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.6167 time to fit residues: 15.0644 Evaluate side-chains 23 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.115929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103030 restraints weight = 2224.737| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.22 r_work: 0.3442 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1530 Z= 0.096 Angle : 0.572 4.660 2058 Z= 0.301 Chirality : 0.047 0.133 249 Planarity : 0.002 0.018 276 Dihedral : 4.463 15.966 222 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 143 HIS 0.001 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 1530) covalent geometry : angle 0.57222 ( 2058) hydrogen bonds : bond 0.01981 ( 9) hydrogen bonds : angle 4.82798 ( 27) *********************** 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: 3 poor density : 28 time to evaluate : 0.070 Fit side-chains REVERT: A 122 LYS cc_start: 0.8340 (mttp) cc_final: 0.7922 (mtpp) REVERT: A 151 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6925 (mt) REVERT: B 122 LYS cc_start: 0.8222 (mttp) cc_final: 0.7809 (mtpp) REVERT: B 126 LEU cc_start: 0.8526 (mt) cc_final: 0.8321 (mp) REVERT: C 122 LYS cc_start: 0.8273 (mttp) cc_final: 0.7920 (mtpm) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.5075 time to fit residues: 14.9753 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 : 0.062 ------------------------------------------------------------------------------- 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: 0.0020 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.112742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099966 restraints weight = 2093.524| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.18 r_work: 0.3367 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1530 Z= 0.150 Angle : 0.637 4.756 2058 Z= 0.336 Chirality : 0.049 0.138 249 Planarity : 0.003 0.021 276 Dihedral : 4.820 17.004 222 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.31 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 HIS 0.001 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 1530) covalent geometry : angle 0.63682 ( 2058) hydrogen bonds : bond 0.02538 ( 9) hydrogen bonds : angle 5.21475 ( 27) ********************** 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 29 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.080 Fit side-chains REVERT: A 122 LYS cc_start: 0.8371 (mttp) cc_final: 0.7965 (mtpp) REVERT: A 151 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7252 (mt) REVERT: B 122 LYS cc_start: 0.8245 (mttp) cc_final: 0.7810 (mtpp) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.4188 time to fit residues: 11.1194 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 : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 121 GLU 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 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103226 restraints weight = 2027.327| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.16 r_work: 0.3426 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1530 Z= 0.111 Angle : 0.599 4.752 2058 Z= 0.317 Chirality : 0.049 0.163 249 Planarity : 0.003 0.019 276 Dihedral : 4.490 15.196 222 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.49), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 HIS 0.001 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 1530) covalent geometry : angle 0.59920 ( 2058) hydrogen bonds : bond 0.02090 ( 9) hydrogen bonds : angle 4.96869 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 928.22 seconds wall clock time: 16 minutes 53.36 seconds (1013.36 seconds total)