Starting phenix.real_space_refine on Fri Oct 10 10:17:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sek_40419/10_2025/8sek_40419.map" } resolution = 3.5 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= -0.005 sd= 0.978 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 10 5.16 5 C 1540 2.51 5 N 400 2.21 5 O 430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.57, per 1000 atoms: 0.24 Number of scatterers: 2380 At special positions: 0 Unit cell: (75.888, 60.078, 41.106, 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 10 16.00 O 430 8.00 N 400 7.00 C 1540 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: 0.22 Conformation dependent library (CDL) restraints added in 147.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.558A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.890A pdb=" N ILE C 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE E 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY E 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE G 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY G 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE I 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE G 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY I 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.558A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AA7, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.889A pdb=" N ILE D 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY D 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE F 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY F 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE H 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY H 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE J 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY J 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 0.37 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 515 1.44 - 1.56: 1210 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 2420 Sorted by residual: bond pdb=" CB HIS G 13 " pdb=" CG HIS G 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS E 13 " pdb=" CG HIS E 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS D 13 " pdb=" CG HIS D 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 bond pdb=" CB HIS C 13 " pdb=" CG HIS C 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" CB HIS B 13 " pdb=" CG HIS B 13 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.48e+01 ... (remaining 2415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 2374 1.97 - 3.95: 578 3.95 - 5.92: 148 5.92 - 7.89: 100 7.89 - 9.87: 50 Bond angle restraints: 3250 Sorted by residual: angle pdb=" N HIS H 13 " pdb=" CA HIS H 13 " pdb=" C HIS H 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" C HIS G 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" N HIS J 13 " pdb=" CA HIS J 13 " pdb=" C HIS J 13 " ideal model delta sigma weight residual 108.75 116.85 -8.10 9.60e-01 1.09e+00 7.11e+01 angle pdb=" N HIS D 13 " pdb=" CA HIS D 13 " pdb=" C HIS D 13 " ideal model delta sigma weight residual 108.75 116.83 -8.08 9.60e-01 1.09e+00 7.09e+01 angle pdb=" N HIS I 13 " pdb=" CA HIS I 13 " pdb=" C HIS I 13 " ideal model delta sigma weight residual 108.75 116.82 -8.07 9.60e-01 1.09e+00 7.07e+01 ... (remaining 3245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.02: 1190 10.02 - 20.03: 90 20.03 - 30.04: 40 30.04 - 40.06: 10 40.06 - 50.07: 10 Dihedral angle restraints: 1340 sinusoidal: 500 harmonic: 840 Sorted by residual: dihedral pdb=" C PHE G 20 " pdb=" N PHE G 20 " pdb=" CA PHE G 20 " pdb=" CB PHE G 20 " ideal model delta harmonic sigma weight residual -122.60 -116.11 -6.49 0 2.50e+00 1.60e-01 6.74e+00 dihedral pdb=" C PHE E 20 " pdb=" N PHE E 20 " pdb=" CA PHE E 20 " pdb=" CB PHE E 20 " ideal model delta harmonic sigma weight residual -122.60 -116.13 -6.47 0 2.50e+00 1.60e-01 6.70e+00 dihedral pdb=" C PHE I 20 " pdb=" N PHE I 20 " pdb=" CA PHE I 20 " pdb=" CB PHE I 20 " ideal model delta harmonic sigma weight residual -122.60 -116.13 -6.47 0 2.50e+00 1.60e-01 6.69e+00 ... (remaining 1337 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.074: 159 0.074 - 0.143: 121 0.143 - 0.211: 20 0.211 - 0.280: 30 0.280 - 0.348: 30 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA PHE J 19 " pdb=" N PHE J 19 " pdb=" C PHE J 19 " pdb=" CB PHE J 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE B 19 " pdb=" N PHE B 19 " pdb=" C PHE B 19 " pdb=" CB PHE B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE E 19 " pdb=" N PHE E 19 " pdb=" C PHE E 19 " pdb=" CB PHE E 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 357 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C VAL A 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL A 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL A 40 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C VAL C 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL C 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL C 40 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 40 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.71e+01 pdb=" C VAL G 40 " 0.119 2.00e-02 2.50e+03 pdb=" O VAL G 40 " -0.043 2.00e-02 2.50e+03 pdb=" OXT VAL G 40 " -0.042 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1058 2.90 - 3.40: 2137 3.40 - 3.90: 4274 3.90 - 4.40: 4695 4.40 - 4.90: 8761 Nonbonded interactions: 20925 Sorted by model distance: nonbonded pdb=" N LYS C 28 " pdb=" N GLY C 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS I 28 " pdb=" N GLY I 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS E 28 " pdb=" N GLY E 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS F 28 " pdb=" N GLY F 29 " model vdw 2.397 2.560 nonbonded pdb=" N LYS B 28 " pdb=" N GLY B 29 " model vdw 2.397 2.560 ... (remaining 20920 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.080 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.840 Find NCS groups from input model: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.032 0.169 2420 Z= 1.654 Angle : 2.389 9.868 3250 Z= 1.617 Chirality : 0.140 0.348 360 Planarity : 0.013 0.069 420 Dihedral : 10.425 50.073 820 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.19 (0.40), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.012 TYR F 10 PHE 0.018 0.005 PHE B 20 HIS 0.007 0.003 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.03231 ( 2420) covalent geometry : angle 2.38935 ( 3250) hydrogen bonds : bond 0.06993 ( 48) hydrogen bonds : angle 7.89583 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: F 18 VAL cc_start: 0.8270 (m) cc_final: 0.7985 (p) REVERT: G 10 TYR cc_start: 0.6926 (p90) cc_final: 0.6718 (p90) REVERT: H 19 PHE cc_start: 0.8102 (p90) cc_final: 0.7820 (p90) REVERT: I 28 LYS cc_start: 0.7658 (ptpt) cc_final: 0.5889 (mmtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0606 time to fit residues: 6.2725 Evaluate side-chains 67 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.194969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.180626 restraints weight = 2969.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.185430 restraints weight = 1060.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.188439 restraints weight = 532.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.190396 restraints weight = 322.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.191637 restraints weight = 215.745| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 2420 Z= 0.297 Angle : 0.889 10.228 3250 Z= 0.503 Chirality : 0.065 0.257 360 Planarity : 0.003 0.012 420 Dihedral : 7.513 23.769 330 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 3.75 % Allowed : 11.67 % Favored : 84.58 % 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: -4.36 (0.29), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR A 10 PHE 0.022 0.004 PHE E 20 HIS 0.006 0.002 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 2420) covalent geometry : angle 0.88875 ( 3250) hydrogen bonds : bond 0.02437 ( 48) hydrogen bonds : angle 5.23071 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7414 (p90) REVERT: C 34 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8639 (tt) REVERT: D 19 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7280 (p90) REVERT: I 28 LYS cc_start: 0.7790 (ptpt) cc_final: 0.5276 (mmtt) outliers start: 9 outliers final: 2 residues processed: 76 average time/residue: 0.0402 time to fit residues: 3.9344 Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.5017 r_free = 0.5017 target = 0.203024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.188664 restraints weight = 2885.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.193376 restraints weight = 1064.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.196295 restraints weight = 538.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.198246 restraints weight = 328.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.199507 restraints weight = 216.346| |-----------------------------------------------------------------------------| r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2420 Z= 0.191 Angle : 0.692 5.163 3250 Z= 0.396 Chirality : 0.059 0.220 360 Planarity : 0.003 0.016 420 Dihedral : 8.029 30.742 330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 5.42 % Allowed : 10.00 % Favored : 84.58 % 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: -4.27 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR I 10 PHE 0.020 0.003 PHE E 19 HIS 0.008 0.002 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 2420) covalent geometry : angle 0.69185 ( 3250) hydrogen bonds : bond 0.02481 ( 48) hydrogen bonds : angle 4.95952 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7108 (p90) REVERT: B 13 HIS cc_start: 0.7889 (t-90) cc_final: 0.5411 (p-80) REVERT: B 19 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7347 (p90) REVERT: C 19 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7145 (p90) REVERT: D 15 GLN cc_start: 0.8310 (mp10) cc_final: 0.8013 (mp10) REVERT: D 19 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7168 (p90) REVERT: E 19 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7668 (p90) REVERT: I 28 LYS cc_start: 0.7803 (ptpt) cc_final: 0.5214 (mmtt) REVERT: J 13 HIS cc_start: 0.7376 (t-90) cc_final: 0.7057 (t-90) outliers start: 13 outliers final: 3 residues processed: 74 average time/residue: 0.0404 time to fit residues: 3.8894 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.5077 r_free = 0.5077 target = 0.207997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.194092 restraints weight = 2852.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.198866 restraints weight = 1033.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.201959 restraints weight = 514.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.203690 restraints weight = 298.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.204905 restraints weight = 198.393| |-----------------------------------------------------------------------------| r_work (final): 0.5053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2420 Z= 0.159 Angle : 0.631 4.382 3250 Z= 0.361 Chirality : 0.059 0.229 360 Planarity : 0.002 0.021 420 Dihedral : 8.245 34.801 330 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.58 % Allowed : 15.83 % Favored : 79.58 % 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: -4.17 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR I 10 PHE 0.037 0.003 PHE F 19 HIS 0.007 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2420) covalent geometry : angle 0.63055 ( 3250) hydrogen bonds : bond 0.02278 ( 48) hydrogen bonds : angle 4.84684 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6743 (p90) REVERT: B 13 HIS cc_start: 0.7664 (t-90) cc_final: 0.5336 (p-80) REVERT: C 19 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7109 (p90) REVERT: C 34 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8612 (tt) REVERT: D 15 GLN cc_start: 0.8475 (mp10) cc_final: 0.7862 (mp10) REVERT: D 19 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.7110 (p90) REVERT: E 19 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7676 (p90) REVERT: H 19 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7944 (p90) REVERT: I 28 LYS cc_start: 0.7548 (ptpt) cc_final: 0.5021 (mmtt) outliers start: 11 outliers final: 0 residues processed: 73 average time/residue: 0.0400 time to fit residues: 3.7711 Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 19 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.198436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.184349 restraints weight = 2880.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.188845 restraints weight = 1100.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.191818 restraints weight = 570.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.193707 restraints weight = 347.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.194830 restraints weight = 230.443| |-----------------------------------------------------------------------------| r_work (final): 0.4998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2420 Z= 0.210 Angle : 0.647 3.981 3250 Z= 0.373 Chirality : 0.060 0.264 360 Planarity : 0.003 0.020 420 Dihedral : 8.245 35.555 330 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Rotamer: Outliers : 6.25 % Allowed : 17.92 % Favored : 75.83 % 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: -4.19 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 10 PHE 0.025 0.003 PHE F 19 HIS 0.007 0.002 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 2420) covalent geometry : angle 0.64739 ( 3250) hydrogen bonds : bond 0.02045 ( 48) hydrogen bonds : angle 4.21919 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6836 (p90) REVERT: B 13 HIS cc_start: 0.7829 (t-90) cc_final: 0.5267 (p-80) REVERT: C 19 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7245 (p90) REVERT: D 19 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7302 (p90) REVERT: E 19 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7746 (p90) REVERT: H 10 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6032 (p90) REVERT: I 28 LYS cc_start: 0.7572 (ptpt) cc_final: 0.5301 (mmtt) outliers start: 15 outliers final: 5 residues processed: 75 average time/residue: 0.0400 time to fit residues: 3.8866 Evaluate side-chains 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.204562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.190730 restraints weight = 2944.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.195873 restraints weight = 1128.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.198878 restraints weight = 570.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.200654 restraints weight = 334.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.201696 restraints weight = 218.726| |-----------------------------------------------------------------------------| r_work (final): 0.5081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2420 Z= 0.157 Angle : 0.644 7.642 3250 Z= 0.356 Chirality : 0.060 0.262 360 Planarity : 0.002 0.018 420 Dihedral : 8.289 37.866 330 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Rotamer: Outliers : 3.33 % Allowed : 21.67 % Favored : 75.00 % 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: -4.20 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 10 PHE 0.034 0.003 PHE F 19 HIS 0.006 0.001 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2420) covalent geometry : angle 0.64353 ( 3250) hydrogen bonds : bond 0.02160 ( 48) hydrogen bonds : angle 4.50961 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6877 (ttt) cc_final: 0.6529 (ttt) REVERT: B 13 HIS cc_start: 0.7522 (t-90) cc_final: 0.5071 (p-80) REVERT: C 19 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6938 (p90) REVERT: D 15 GLN cc_start: 0.8523 (mp10) cc_final: 0.7817 (mp10) REVERT: E 19 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7626 (p90) REVERT: H 10 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6121 (p90) REVERT: I 28 LYS cc_start: 0.7462 (ptpt) cc_final: 0.5148 (mmtt) outliers start: 8 outliers final: 1 residues processed: 72 average time/residue: 0.0405 time to fit residues: 3.7813 Evaluate side-chains 62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 19 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.207029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.193170 restraints weight = 2962.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.198380 restraints weight = 1155.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.201481 restraints weight = 578.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.203220 restraints weight = 336.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.204314 restraints weight = 216.865| |-----------------------------------------------------------------------------| r_work (final): 0.5114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2420 Z= 0.151 Angle : 0.663 5.870 3250 Z= 0.369 Chirality : 0.060 0.270 360 Planarity : 0.002 0.017 420 Dihedral : 8.546 39.869 330 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 3.75 % Allowed : 22.50 % Favored : 73.75 % 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: -4.21 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 10 PHE 0.039 0.003 PHE F 19 HIS 0.011 0.002 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2420) covalent geometry : angle 0.66319 ( 3250) hydrogen bonds : bond 0.02171 ( 48) hydrogen bonds : angle 4.63495 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6735 (ttt) cc_final: 0.6510 (ttt) REVERT: B 13 HIS cc_start: 0.7485 (t-90) cc_final: 0.4986 (p-80) REVERT: B 15 GLN cc_start: 0.8485 (mp10) cc_final: 0.8143 (mp10) REVERT: E 19 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7669 (p90) REVERT: G 19 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8053 (p90) REVERT: H 10 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6163 (p90) REVERT: I 28 LYS cc_start: 0.7485 (ptpt) cc_final: 0.5173 (mmtt) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 0.0412 time to fit residues: 3.6336 Evaluate side-chains 68 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.211223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.197186 restraints weight = 2877.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.202126 restraints weight = 1127.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.205294 restraints weight = 576.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.207099 restraints weight = 337.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.208272 restraints weight = 219.356| |-----------------------------------------------------------------------------| r_work (final): 0.5156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2420 Z= 0.148 Angle : 0.649 6.816 3250 Z= 0.359 Chirality : 0.060 0.285 360 Planarity : 0.003 0.019 420 Dihedral : 8.584 39.886 330 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 3.75 % Allowed : 25.00 % Favored : 71.25 % 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: -4.19 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 10 PHE 0.041 0.003 PHE F 19 HIS 0.011 0.002 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2420) covalent geometry : angle 0.64883 ( 3250) hydrogen bonds : bond 0.02279 ( 48) hydrogen bonds : angle 4.71602 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6735 (ttt) cc_final: 0.6488 (ttt) REVERT: B 13 HIS cc_start: 0.7399 (t-90) cc_final: 0.4998 (p-80) REVERT: B 15 GLN cc_start: 0.8619 (mp10) cc_final: 0.8140 (mp10) REVERT: E 19 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7575 (p90) REVERT: G 19 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.8011 (p90) REVERT: H 10 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.6183 (p90) REVERT: I 28 LYS cc_start: 0.7454 (ptpt) cc_final: 0.5112 (mmtt) outliers start: 9 outliers final: 2 residues processed: 69 average time/residue: 0.0422 time to fit residues: 3.7024 Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.203547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.189825 restraints weight = 3056.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.194861 restraints weight = 1174.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.197825 restraints weight = 593.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.199584 restraints weight = 352.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.200771 restraints weight = 231.129| |-----------------------------------------------------------------------------| r_work (final): 0.5069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2420 Z= 0.174 Angle : 0.665 6.875 3250 Z= 0.371 Chirality : 0.061 0.296 360 Planarity : 0.003 0.016 420 Dihedral : 8.526 38.549 330 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 3.75 % Allowed : 24.58 % Favored : 71.67 % 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: -4.18 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR A 10 PHE 0.030 0.003 PHE C 19 HIS 0.016 0.003 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 2420) covalent geometry : angle 0.66473 ( 3250) hydrogen bonds : bond 0.02436 ( 48) hydrogen bonds : angle 4.54208 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.6865 (ttt) cc_final: 0.6600 (ttt) REVERT: B 13 HIS cc_start: 0.7406 (t-90) cc_final: 0.4920 (p-80) REVERT: B 15 GLN cc_start: 0.8643 (mp10) cc_final: 0.8096 (mp10) REVERT: B 22 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7180 (mm-30) REVERT: G 19 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7875 (p90) REVERT: H 10 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6245 (p90) REVERT: I 28 LYS cc_start: 0.7651 (ptpt) cc_final: 0.5291 (mmtt) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.0392 time to fit residues: 3.3146 Evaluate side-chains 65 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.186181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.173018 restraints weight = 3142.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.177408 restraints weight = 1206.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.180268 restraints weight = 623.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.182076 restraints weight = 378.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.183110 restraints weight = 250.708| |-----------------------------------------------------------------------------| r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 2420 Z= 0.277 Angle : 0.763 6.603 3250 Z= 0.429 Chirality : 0.062 0.304 360 Planarity : 0.003 0.018 420 Dihedral : 8.488 34.063 330 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 2.92 % Allowed : 25.42 % Favored : 71.67 % 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: -4.54 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR I 10 PHE 0.038 0.004 PHE C 19 HIS 0.022 0.003 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 2420) covalent geometry : angle 0.76308 ( 3250) hydrogen bonds : bond 0.02656 ( 48) hydrogen bonds : angle 4.20790 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7144 (ttt) cc_final: 0.6755 (ttt) REVERT: B 13 HIS cc_start: 0.7818 (t-90) cc_final: 0.5260 (p-80) REVERT: B 15 GLN cc_start: 0.8943 (mp10) cc_final: 0.8122 (mp10) REVERT: H 10 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6272 (p90) REVERT: I 28 LYS cc_start: 0.7722 (ptpt) cc_final: 0.5439 (mmtt) REVERT: J 20 PHE cc_start: 0.7994 (m-10) cc_final: 0.7754 (m-10) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.0333 time to fit residues: 2.8042 Evaluate side-chains 64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.197022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.184123 restraints weight = 3096.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.188856 restraints weight = 1153.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.191823 restraints weight = 583.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.193576 restraints weight = 333.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.194521 restraints weight = 207.125| |-----------------------------------------------------------------------------| r_work (final): 0.5032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2420 Z= 0.174 Angle : 0.706 8.240 3250 Z= 0.387 Chirality : 0.060 0.297 360 Planarity : 0.003 0.018 420 Dihedral : 8.506 35.862 330 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer: Outliers : 2.50 % Allowed : 26.25 % Favored : 71.25 % 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: -4.51 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.029 0.003 PHE C 19 HIS 0.016 0.003 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2420) covalent geometry : angle 0.70593 ( 3250) hydrogen bonds : bond 0.02577 ( 48) hydrogen bonds : angle 4.54101 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 661.31 seconds wall clock time: 12 minutes 1.71 seconds (721.71 seconds total)