Starting phenix.real_space_refine on Mon Feb 10 20:40:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sek_40419/02_2025/8sek_40419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sek_40419/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sek_40419/02_2025/8sek_40419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sek_40419/02_2025/8sek_40419.map" model { file = "/net/cci-nas-00/data/ceres_data/8sek_40419/02_2025/8sek_40419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sek_40419/02_2025/8sek_40419_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.28, per 1000 atoms: 0.54 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: 0.48 Conformation dependent library (CDL) restraints added in 224.2 milliseconds 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: 0.36 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: 0.56 Time building geometry restraints manager: 0.56 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.020 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- 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= 2.143 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (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 HIS 0.007 0.003 HIS H 13 PHE 0.018 0.005 PHE B 20 TYR 0.025 0.012 TYR F 10 *********************** 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 : 0.285 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: 0.1465 time to fit residues: 14.8330 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.5003 r_free = 0.5003 target = 0.202995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.189003 restraints weight = 2982.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.193751 restraints weight = 1044.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.196796 restraints weight = 522.803| |-----------------------------------------------------------------------------| r_work (final): 0.4971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2420 Z= 0.383 Angle : 0.848 10.012 3250 Z= 0.478 Chirality : 0.065 0.250 360 Planarity : 0.003 0.013 420 Dihedral : 7.649 23.832 330 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 3.75 % Allowed : 10.83 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.23), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 14 PHE 0.018 0.004 PHE D 19 TYR 0.013 0.002 TYR A 10 *********************** 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 : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7346 (p90) REVERT: C 34 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8591 (tt) REVERT: D 19 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7292 (p90) REVERT: I 28 LYS cc_start: 0.7710 (ptpt) cc_final: 0.5197 (mmtt) outliers start: 9 outliers final: 2 residues processed: 76 average time/residue: 0.0985 time to fit residues: 9.4069 Evaluate side-chains 61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 3 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 = 0.4967 r_free = 0.4967 target = 0.196655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.182841 restraints weight = 3036.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.187537 restraints weight = 1139.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.190581 restraints weight = 573.552| |-----------------------------------------------------------------------------| r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2420 Z= 0.353 Angle : 0.701 4.955 3250 Z= 0.403 Chirality : 0.059 0.227 360 Planarity : 0.003 0.015 420 Dihedral : 7.989 31.255 330 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.58 % Allowed : 12.92 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 13 PHE 0.022 0.003 PHE E 19 TYR 0.010 0.002 TYR I 10 *********************** 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 75 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7259 (p90) REVERT: B 19 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7457 (p90) REVERT: C 19 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7160 (p90) REVERT: D 19 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7342 (p90) REVERT: E 19 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7703 (p90) REVERT: F 19 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7676 (p90) REVERT: G 19 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8223 (p90) REVERT: I 28 LYS cc_start: 0.7713 (ptpt) cc_final: 0.5199 (mmtt) REVERT: J 13 HIS cc_start: 0.7479 (t-90) cc_final: 0.7176 (t70) outliers start: 11 outliers final: 3 residues processed: 71 average time/residue: 0.1000 time to fit residues: 8.9567 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 : 0.250 ------------------------------------------------------------------------------- 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 F residue 19 PHE Chi-restraints excluded: chain G 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 17 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4997 r_free = 0.4997 target = 0.199059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.185428 restraints weight = 2938.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.190215 restraints weight = 1108.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.193315 restraints weight = 563.748| |-----------------------------------------------------------------------------| r_work (final): 0.4963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2420 Z= 0.311 Angle : 0.655 5.257 3250 Z= 0.375 Chirality : 0.059 0.239 360 Planarity : 0.003 0.022 420 Dihedral : 8.085 34.137 330 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.83 % Allowed : 14.17 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 14 PHE 0.019 0.003 PHE E 19 TYR 0.009 0.002 TYR I 10 *********************** 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 86 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6998 (p90) REVERT: B 13 HIS cc_start: 0.7728 (t-90) cc_final: 0.5271 (p-80) REVERT: B 19 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7282 (p90) REVERT: C 19 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7218 (p90) REVERT: E 19 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (p90) REVERT: F 32 ILE cc_start: 0.8890 (mt) cc_final: 0.8643 (mt) REVERT: G 19 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8157 (p90) REVERT: I 28 LYS cc_start: 0.7658 (ptpt) cc_final: 0.5153 (mmtt) outliers start: 14 outliers final: 4 residues processed: 79 average time/residue: 0.0978 time to fit residues: 9.6495 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 : 0.301 ------------------------------------------------------------------------------- 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 11 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4990 r_free = 0.4990 target = 0.196038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.182811 restraints weight = 3006.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.187452 restraints weight = 1145.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.190349 restraints weight = 580.364| |-----------------------------------------------------------------------------| r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2420 Z= 0.330 Angle : 0.657 4.809 3250 Z= 0.376 Chirality : 0.060 0.256 360 Planarity : 0.003 0.020 420 Dihedral : 8.175 35.196 330 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 14 PHE 0.036 0.003 PHE F 19 TYR 0.008 0.002 TYR A 10 *********************** 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 82 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6916 (p90) REVERT: A 35 MET cc_start: 0.6895 (ttt) cc_final: 0.6518 (ttt) REVERT: B 13 HIS cc_start: 0.7742 (t-90) cc_final: 0.5130 (p-80) REVERT: B 19 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7169 (p90) REVERT: C 19 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7174 (p90) REVERT: E 19 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7703 (p90) REVERT: G 19 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8104 (p90) REVERT: G 34 LEU cc_start: 0.8916 (tp) cc_final: 0.8666 (tt) REVERT: H 10 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6072 (p90) REVERT: I 28 LYS cc_start: 0.7552 (ptpt) cc_final: 0.5271 (mmtt) outliers start: 15 outliers final: 5 residues processed: 76 average time/residue: 0.0961 time to fit residues: 9.1747 Evaluate side-chains 74 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 11 GLU Chi-restraints excluded: chain E residue 11 GLU 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 J residue 15 GLN Chi-restraints excluded: chain J residue 19 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5034 r_free = 0.5034 target = 0.198167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.184368 restraints weight = 2972.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.189223 restraints weight = 1144.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.192244 restraints weight = 587.756| |-----------------------------------------------------------------------------| r_work (final): 0.4999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4578 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= 0.287 Angle : 0.651 6.325 3250 Z= 0.366 Chirality : 0.059 0.265 360 Planarity : 0.003 0.018 420 Dihedral : 8.263 36.369 330 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.67 % Favored : 84.33 % Rotamer: Outliers : 7.08 % Allowed : 18.33 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 14 PHE 0.037 0.003 PHE F 19 TYR 0.008 0.001 TYR I 10 *********************** 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 79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7004 (ttt) cc_final: 0.6673 (ttt) REVERT: B 13 HIS cc_start: 0.7653 (t-90) cc_final: 0.5030 (p-80) REVERT: B 15 GLN cc_start: 0.8611 (mp10) cc_final: 0.7933 (mp10) REVERT: B 19 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7165 (p90) REVERT: C 19 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7047 (p90) REVERT: E 19 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7613 (p90) REVERT: F 15 GLN cc_start: 0.8765 (mp10) cc_final: 0.8056 (mp10) REVERT: H 10 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6254 (p90) REVERT: I 28 LYS cc_start: 0.7551 (ptpt) cc_final: 0.5253 (mmtt) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 0.0915 time to fit residues: 8.4289 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E 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 I residue 34 LEU Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0170 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5102 r_free = 0.5102 target = 0.205912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.191056 restraints weight = 2867.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.195994 restraints weight = 1086.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.199143 restraints weight = 560.557| |-----------------------------------------------------------------------------| r_work (final): 0.5076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4865 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= 0.238 Angle : 0.622 5.376 3250 Z= 0.347 Chirality : 0.060 0.276 360 Planarity : 0.002 0.017 420 Dihedral : 8.419 38.528 330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 5.42 % Allowed : 21.25 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.040 0.003 PHE F 19 TYR 0.008 0.001 TYR E 10 *********************** 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 78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6782 (ttt) cc_final: 0.6444 (ttt) REVERT: B 13 HIS cc_start: 0.7447 (t-90) cc_final: 0.4923 (p-80) REVERT: B 15 GLN cc_start: 0.8443 (mp10) cc_final: 0.8004 (mp10) REVERT: C 19 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7069 (p90) REVERT: D 13 HIS cc_start: 0.7403 (t-90) cc_final: 0.7197 (t-90) REVERT: D 15 GLN cc_start: 0.8410 (mp10) cc_final: 0.8055 (mp10) REVERT: E 19 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7558 (p90) REVERT: H 10 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.6214 (p90) REVERT: I 28 LYS cc_start: 0.7468 (ptpt) cc_final: 0.5149 (mmtt) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.0979 time to fit residues: 8.9067 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 : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E 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 I residue 34 LEU 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 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4940 r_free = 0.4940 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.173625 restraints weight = 3209.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.178071 restraints weight = 1225.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.180951 restraints weight = 629.312| |-----------------------------------------------------------------------------| r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 2420 Z= 0.460 Angle : 0.725 5.314 3250 Z= 0.412 Chirality : 0.061 0.292 360 Planarity : 0.003 0.022 420 Dihedral : 8.436 34.174 330 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 5.42 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.33), 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 HIS 0.021 0.003 HIS J 14 PHE 0.051 0.004 PHE F 19 TYR 0.009 0.002 TYR A 10 *********************** 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 73 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6917 (ttt) cc_final: 0.6587 (ttt) REVERT: B 13 HIS cc_start: 0.7896 (t-90) cc_final: 0.5443 (p90) REVERT: C 19 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7488 (p90) REVERT: E 18 VAL cc_start: 0.8739 (m) cc_final: 0.8388 (t) REVERT: E 19 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7729 (p90) REVERT: E 35 MET cc_start: 0.8083 (ttt) cc_final: 0.7750 (ttt) REVERT: F 15 GLN cc_start: 0.8747 (mp10) cc_final: 0.8040 (mp10) REVERT: H 10 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.6377 (p90) REVERT: I 28 LYS cc_start: 0.7818 (ptpt) cc_final: 0.5578 (mmtt) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.0999 time to fit residues: 8.4441 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E 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 I residue 34 LEU Chi-restraints excluded: chain J residue 19 PHE 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 11 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.196062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.183167 restraints weight = 3059.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.187767 restraints weight = 1144.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.190649 restraints weight = 579.544| |-----------------------------------------------------------------------------| r_work (final): 0.4991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2420 Z= 0.290 Angle : 0.693 8.022 3250 Z= 0.387 Chirality : 0.061 0.294 360 Planarity : 0.003 0.022 420 Dihedral : 8.445 35.576 330 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 5.42 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS J 14 PHE 0.050 0.003 PHE F 19 TYR 0.007 0.001 TYR I 10 *********************** 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 73 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6868 (ttt) cc_final: 0.6531 (ttt) REVERT: B 13 HIS cc_start: 0.7768 (t-90) cc_final: 0.5471 (p-80) REVERT: C 19 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7151 (p90) REVERT: E 19 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7546 (p90) REVERT: E 35 MET cc_start: 0.8105 (ttt) cc_final: 0.7679 (ttt) REVERT: G 19 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.8059 (p90) REVERT: G 32 ILE cc_start: 0.8841 (mt) cc_final: 0.8507 (pt) REVERT: H 10 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6187 (p90) REVERT: I 28 LYS cc_start: 0.7527 (ptpt) cc_final: 0.5196 (mmtt) outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.1000 time to fit residues: 8.5911 Evaluate side-chains 64 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 11 GLU 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 I residue 34 LEU 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 6 optimal weight: 7.9990 chunk 15 optimal weight: 0.0060 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.203078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.189767 restraints weight = 2877.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.194461 restraints weight = 1105.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.197464 restraints weight = 562.379| |-----------------------------------------------------------------------------| r_work (final): 0.5092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2420 Z= 0.256 Angle : 0.678 6.447 3250 Z= 0.373 Chirality : 0.061 0.291 360 Planarity : 0.003 0.018 420 Dihedral : 8.574 37.817 330 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS J 14 PHE 0.042 0.003 PHE F 19 TYR 0.006 0.001 TYR I 10 ********************** 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 67 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7001 (ttt) cc_final: 0.6687 (ttt) REVERT: B 13 HIS cc_start: 0.7569 (t-90) cc_final: 0.5281 (p-80) REVERT: E 19 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7516 (p90) REVERT: G 32 ILE cc_start: 0.8804 (mt) cc_final: 0.8514 (pt) REVERT: H 10 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6295 (p90) REVERT: I 28 LYS cc_start: 0.7625 (ptpt) cc_final: 0.5257 (mmtt) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.1007 time to fit residues: 8.2069 Evaluate side-chains 62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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 15 GLN Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 34 LEU 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 23 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** J 14 HIS ** 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 = 0.5040 r_free = 0.5040 target = 0.195923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.182966 restraints weight = 3072.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.187504 restraints weight = 1146.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.190356 restraints weight = 582.729| |-----------------------------------------------------------------------------| r_work (final): 0.4998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2420 Z= 0.361 Angle : 0.714 6.540 3250 Z= 0.396 Chirality : 0.061 0.299 360 Planarity : 0.003 0.020 420 Dihedral : 8.565 36.274 330 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 3.75 % Allowed : 25.83 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.003 HIS J 14 PHE 0.047 0.004 PHE F 19 TYR 0.007 0.002 TYR I 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.63 seconds wall clock time: 20 minutes 27.00 seconds (1227.00 seconds total)