Starting phenix.real_space_refine on Wed Mar 5 15:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sek_40419/03_2025/8sek_40419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sek_40419/03_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_40419/03_2025/8sek_40419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sek_40419/03_2025/8sek_40419.map" model { file = "/net/cci-nas-00/data/ceres_data/8sek_40419/03_2025/8sek_40419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sek_40419/03_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-5624/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: 1.29, 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: 0.58 Conformation dependent library (CDL) restraints added in 303.5 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: 0.42 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: 0.59 Time building geometry restraints manager: 0.66 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 10.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- 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 : 0.262 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: 0.1378 time to fit residues: 14.0465 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 : 0.273 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.189010 restraints weight = 2982.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.193756 restraints weight = 1044.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.196863 restraints weight = 522.473| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7342 (p90) REVERT: C 34 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8603 (tt) REVERT: D 19 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7291 (p90) REVERT: I 28 LYS cc_start: 0.7713 (ptpt) cc_final: 0.5200 (mmtt) outliers start: 9 outliers final: 2 residues processed: 76 average time/residue: 0.0934 time to fit residues: 8.9758 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 : 0.266 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4899 r_free = 0.4899 target = 0.187862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.173989 restraints weight = 3031.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.178589 restraints weight = 1165.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.181593 restraints weight = 601.497| |-----------------------------------------------------------------------------| r_work (final): 0.4857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3671 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= 0.474 Angle : 0.750 5.926 3250 Z= 0.433 Chirality : 0.061 0.248 360 Planarity : 0.003 0.015 420 Dihedral : 8.043 29.887 330 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.58 % Allowed : 13.33 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 14 PHE 0.024 0.004 PHE E 19 TYR 0.012 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 78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7393 (p90) REVERT: A 34 LEU cc_start: 0.9104 (tp) cc_final: 0.8904 (tt) REVERT: B 13 HIS cc_start: 0.7886 (t-90) cc_final: 0.5225 (p-80) REVERT: B 19 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7626 (p90) REVERT: C 19 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7288 (p90) REVERT: D 19 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7394 (p90) REVERT: E 18 VAL cc_start: 0.8710 (m) cc_final: 0.8409 (t) REVERT: E 19 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7802 (p90) REVERT: F 19 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7680 (p90) REVERT: G 19 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (p90) REVERT: I 28 LYS cc_start: 0.7898 (ptpt) cc_final: 0.5376 (mmtt) outliers start: 11 outliers final: 3 residues processed: 74 average time/residue: 0.1014 time to fit residues: 9.5301 Evaluate side-chains 74 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.5027 r_free = 0.5027 target = 0.199652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.185538 restraints weight = 2918.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.190511 restraints weight = 1100.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.193670 restraints weight = 556.133| |-----------------------------------------------------------------------------| r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4161 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= 0.268 Angle : 0.653 4.443 3250 Z= 0.374 Chirality : 0.059 0.240 360 Planarity : 0.002 0.023 420 Dihedral : 8.080 33.773 330 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.42 % Allowed : 14.17 % Favored : 80.42 % 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: -4.33 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.018 0.003 PHE E 19 TYR 0.008 0.001 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 83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7007 (p90) REVERT: B 13 HIS cc_start: 0.7742 (t-90) cc_final: 0.5273 (p-80) REVERT: C 19 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7035 (p90) REVERT: E 18 VAL cc_start: 0.8713 (m) cc_final: 0.8428 (t) REVERT: E 19 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7558 (p90) REVERT: F 32 ILE cc_start: 0.8899 (mt) cc_final: 0.8668 (mt) REVERT: G 19 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8116 (p90) REVERT: H 10 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6119 (p90) REVERT: I 28 LYS cc_start: 0.7528 (ptpt) cc_final: 0.5190 (mmtt) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.0825 time to fit residues: 8.2269 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 : 0.248 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 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 = 0.5006 r_free = 0.5006 target = 0.196667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.182733 restraints weight = 2917.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.187348 restraints weight = 1083.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.190269 restraints weight = 553.447| |-----------------------------------------------------------------------------| r_work (final): 0.4970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4362 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= 0.333 Angle : 0.651 4.643 3250 Z= 0.375 Chirality : 0.059 0.261 360 Planarity : 0.003 0.020 420 Dihedral : 8.229 35.809 330 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 5.42 % Allowed : 19.58 % 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 (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: -4.33 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 14 PHE 0.036 0.004 PHE F 19 TYR 0.009 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 81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6922 (p90) REVERT: B 13 HIS cc_start: 0.7793 (t-90) cc_final: 0.5311 (p-80) REVERT: C 19 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7125 (p90) REVERT: E 18 VAL cc_start: 0.8759 (m) cc_final: 0.8448 (t) REVERT: E 19 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7735 (p90) REVERT: G 19 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (p90) REVERT: H 10 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6204 (p90) REVERT: H 15 GLN cc_start: 0.8520 (mp10) cc_final: 0.8224 (mp10) REVERT: I 28 LYS cc_start: 0.7612 (ptpt) cc_final: 0.5317 (mmtt) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.0995 time to fit residues: 9.3956 Evaluate side-chains 73 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 I residue 34 LEU 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: 0.8980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.197566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.184389 restraints weight = 2974.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.189093 restraints weight = 1121.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.192094 restraints weight = 566.774| |-----------------------------------------------------------------------------| r_work (final): 0.4999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4607 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= 0.298 Angle : 0.665 7.802 3250 Z= 0.373 Chirality : 0.059 0.261 360 Planarity : 0.002 0.017 420 Dihedral : 8.309 36.256 330 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.67 % Favored : 84.33 % Rotamer: Outliers : 6.67 % Allowed : 19.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS J 14 PHE 0.039 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 80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6889 (ttt) cc_final: 0.6517 (ttt) REVERT: B 13 HIS cc_start: 0.7740 (t-90) cc_final: 0.5345 (p-80) REVERT: C 19 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7119 (p90) REVERT: E 18 VAL cc_start: 0.8749 (m) cc_final: 0.8490 (t) REVERT: E 19 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7614 (p90) REVERT: F 15 GLN cc_start: 0.8813 (mp10) cc_final: 0.8180 (mp10) REVERT: H 10 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6188 (p90) REVERT: I 28 LYS cc_start: 0.7580 (ptpt) cc_final: 0.5270 (mmtt) outliers start: 16 outliers final: 8 residues processed: 72 average time/residue: 0.0993 time to fit residues: 8.9795 Evaluate side-chains 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 15 GLN Chi-restraints excluded: chain J residue 19 PHE 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: 1.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** 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 = 0.5069 r_free = 0.5069 target = 0.201567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.187413 restraints weight = 2909.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.192105 restraints weight = 1093.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.195220 restraints weight = 560.674| |-----------------------------------------------------------------------------| r_work (final): 0.5036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2420 Z= 0.251 Angle : 0.646 6.339 3250 Z= 0.362 Chirality : 0.060 0.273 360 Planarity : 0.003 0.018 420 Dihedral : 8.402 37.220 330 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.42 % Allowed : 21.67 % Favored : 72.92 % 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: -4.41 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS J 14 PHE 0.041 0.003 PHE F 19 TYR 0.007 0.001 TYR I 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 75 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6856 (ttt) cc_final: 0.6500 (ttt) REVERT: B 13 HIS cc_start: 0.7536 (t-90) cc_final: 0.5012 (p-80) REVERT: B 15 GLN cc_start: 0.8534 (mp10) cc_final: 0.8105 (mp10) REVERT: C 19 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7207 (p90) REVERT: E 19 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7594 (p90) REVERT: F 15 GLN cc_start: 0.8799 (mp10) cc_final: 0.7937 (mp10) REVERT: H 10 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.6123 (p90) REVERT: I 28 LYS cc_start: 0.7457 (ptpt) cc_final: 0.5134 (mmtt) REVERT: J 13 HIS cc_start: 0.7426 (t-90) cc_final: 0.7051 (t-90) outliers start: 13 outliers final: 4 residues processed: 68 average time/residue: 0.1045 time to fit residues: 9.1093 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 : 0.284 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4929 r_free = 0.4929 target = 0.189470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.175477 restraints weight = 3110.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.179789 restraints weight = 1174.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.182683 restraints weight = 607.745| |-----------------------------------------------------------------------------| r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2420 Z= 0.399 Angle : 0.713 7.008 3250 Z= 0.399 Chirality : 0.061 0.299 360 Planarity : 0.003 0.020 420 Dihedral : 8.378 34.328 330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % Rotamer: Outliers : 5.42 % Allowed : 22.08 % Favored : 72.50 % 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: -4.56 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS J 14 PHE 0.048 0.004 PHE F 19 TYR 0.010 0.002 TYR I 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 76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6649 (p90) REVERT: A 35 MET cc_start: 0.6881 (ttt) cc_final: 0.6530 (ttt) REVERT: B 13 HIS cc_start: 0.7852 (t-90) cc_final: 0.5216 (p90) REVERT: B 15 GLN cc_start: 0.8891 (mp10) cc_final: 0.8132 (mp10) REVERT: B 19 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7338 (p90) REVERT: C 19 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7425 (p90) REVERT: E 18 VAL cc_start: 0.8696 (m) cc_final: 0.8362 (t) REVERT: E 19 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7679 (p90) REVERT: F 15 GLN cc_start: 0.8722 (mp10) cc_final: 0.8423 (mp10) REVERT: H 10 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6223 (p90) REVERT: H 15 GLN cc_start: 0.8581 (mp10) cc_final: 0.8225 (mp10) REVERT: I 28 LYS cc_start: 0.7696 (ptpt) cc_final: 0.5432 (mmtt) outliers start: 13 outliers final: 5 residues processed: 71 average time/residue: 0.0919 time to fit residues: 8.2579 Evaluate side-chains 71 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR 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 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 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: 0.9980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5065 r_free = 0.5065 target = 0.200444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.186599 restraints weight = 2930.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.191232 restraints weight = 1093.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.194339 restraints weight = 560.156| |-----------------------------------------------------------------------------| r_work (final): 0.5031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.004 0.027 2420 Z= 0.257 Angle : 0.664 6.536 3250 Z= 0.370 Chirality : 0.061 0.298 360 Planarity : 0.003 0.022 420 Dihedral : 8.404 36.339 330 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 5.00 % Allowed : 22.08 % Favored : 72.92 % 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 (0.33), 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 HIS 0.009 0.002 HIS J 14 PHE 0.051 0.003 PHE F 19 TYR 0.007 0.001 TYR A 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 80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6840 (ttt) cc_final: 0.6485 (ttt) REVERT: B 13 HIS cc_start: 0.7606 (t-90) cc_final: 0.5247 (p-80) REVERT: B 15 GLN cc_start: 0.8489 (mp10) cc_final: 0.8271 (mp10) REVERT: B 19 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6839 (p90) REVERT: D 15 GLN cc_start: 0.8553 (mp10) cc_final: 0.8256 (mp10) REVERT: E 19 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7611 (p90) REVERT: F 15 GLN cc_start: 0.8761 (mp10) cc_final: 0.8464 (mp10) REVERT: H 10 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6179 (p90) REVERT: I 28 LYS cc_start: 0.7619 (ptpt) cc_final: 0.5240 (mmtt) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 0.1172 time to fit residues: 10.9868 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 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 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5122 r_free = 0.5122 target = 0.204294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.191283 restraints weight = 2897.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.196102 restraints weight = 1124.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.199168 restraints weight = 564.125| |-----------------------------------------------------------------------------| r_work (final): 0.5086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2420 Z= 0.249 Angle : 0.694 6.532 3250 Z= 0.381 Chirality : 0.062 0.295 360 Planarity : 0.003 0.019 420 Dihedral : 8.593 37.066 330 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS J 14 PHE 0.044 0.003 PHE F 19 TYR 0.007 0.001 TYR A 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 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6841 (ttt) cc_final: 0.6507 (ttt) REVERT: B 13 HIS cc_start: 0.7489 (t-90) cc_final: 0.5126 (p-80) REVERT: B 15 GLN cc_start: 0.8493 (mp10) cc_final: 0.8279 (mp10) REVERT: B 19 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6761 (p90) REVERT: D 15 GLN cc_start: 0.8557 (mp10) cc_final: 0.8246 (mp10) REVERT: E 19 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7453 (p90) REVERT: F 15 GLN cc_start: 0.8613 (mp10) cc_final: 0.8203 (mp10) REVERT: H 10 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6020 (p90) REVERT: I 28 LYS cc_start: 0.7622 (ptpt) cc_final: 0.5211 (mmtt) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.1008 time to fit residues: 8.3828 Evaluate side-chains 70 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 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 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5095 r_free = 0.5095 target = 0.202650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.188603 restraints weight = 2994.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.193510 restraints weight = 1147.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.196634 restraints weight = 588.076| |-----------------------------------------------------------------------------| r_work (final): 0.5055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5164 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= 0.264 Angle : 0.692 7.365 3250 Z= 0.375 Chirality : 0.060 0.298 360 Planarity : 0.003 0.018 420 Dihedral : 8.559 36.893 330 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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 (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 (0.33), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.25), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS J 14 PHE 0.043 0.003 PHE F 19 TYR 0.007 0.001 TYR I 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.86 seconds wall clock time: 20 minutes 22.07 seconds (1222.07 seconds total)