Starting phenix.real_space_refine on Fri Apr 5 12:50:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_40419_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_40419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_40419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_40419_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sek_40419/04_2024/8sek_40419_neut.pdb" } 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 Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 10 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} Chain: "B" 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} Chain: "C" 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} Chain: "D" 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} Chain: "E" 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} Chain: "F" 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} Chain: "G" 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} Chain: "H" 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} Chain: "I" 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} Chain: "J" 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} Time building chain proxies: 1.68, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 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: 0.89 Conformation dependent library (CDL) restraints added in 410.1 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: 0.34 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: 0.97 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: 101.92 - 107.92: 260 107.92 - 113.93: 1020 113.93 - 119.93: 995 119.93 - 125.93: 955 125.93 - 131.93: 20 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.500 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- 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 fitting. 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: 0.1392 time to fit residues: 14.1848 Evaluate side-chains 67 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2420 Z= 0.413 Angle : 0.877 9.280 3250 Z= 0.500 Chirality : 0.065 0.241 360 Planarity : 0.003 0.014 420 Dihedral : 7.255 23.232 330 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % Rotamer: Outliers : 3.75 % Allowed : 12.08 % Favored : 84.17 % 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: -4.13 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 13 PHE 0.020 0.004 PHE E 20 TYR 0.012 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 77 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7519 (p90) REVERT: C 34 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (tt) REVERT: D 19 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7347 (p90) REVERT: I 28 LYS cc_start: 0.7514 (ptpt) cc_final: 0.5756 (mmtt) outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.1015 time to fit residues: 9.4037 Evaluate side-chains 61 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 22 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3625 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= 0.286 Angle : 0.674 6.068 3250 Z= 0.382 Chirality : 0.059 0.228 360 Planarity : 0.002 0.012 420 Dihedral : 8.079 31.415 330 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 6.25 % Allowed : 10.83 % Favored : 82.92 % 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: -4.14 (0.32), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 14 PHE 0.020 0.003 PHE E 19 TYR 0.010 0.001 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 79 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7063 (p90) REVERT: A 28 LYS cc_start: 0.8379 (ptpp) cc_final: 0.8072 (mtmm) REVERT: B 13 HIS cc_start: 0.6837 (t-90) cc_final: 0.5450 (p-80) REVERT: B 19 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7241 (p90) REVERT: C 19 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7436 (p90) REVERT: E 19 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7760 (p90) REVERT: I 28 LYS cc_start: 0.7633 (ptpt) cc_final: 0.5772 (mmtt) outliers start: 15 outliers final: 3 residues processed: 73 average time/residue: 0.1013 time to fit residues: 9.2175 Evaluate side-chains 66 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 E residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE 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 3 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2420 Z= 0.322 Angle : 0.639 3.755 3250 Z= 0.370 Chirality : 0.059 0.229 360 Planarity : 0.003 0.016 420 Dihedral : 8.146 33.071 330 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.67 % Favored : 82.33 % Rotamer: Outliers : 5.42 % Allowed : 15.83 % Favored : 78.75 % 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: -4.14 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 14 PHE 0.037 0.003 PHE F 19 TYR 0.008 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 74 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6912 (p90) REVERT: A 28 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8176 (mtmm) REVERT: B 13 HIS cc_start: 0.6839 (t-90) cc_final: 0.5450 (p-80) REVERT: C 19 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7404 (p90) REVERT: E 19 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7762 (p90) REVERT: I 28 LYS cc_start: 0.7774 (ptpt) cc_final: 0.5886 (mmtt) outliers start: 13 outliers final: 5 residues processed: 70 average time/residue: 0.0992 time to fit residues: 8.6904 Evaluate side-chains 68 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 H residue 11 GLU Chi-restraints excluded: chain J residue 14 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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** ** I 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2420 Z= 0.254 Angle : 0.613 4.761 3250 Z= 0.353 Chirality : 0.059 0.256 360 Planarity : 0.002 0.015 420 Dihedral : 8.281 36.324 330 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer: Outliers : 5.42 % Allowed : 20.00 % 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: -4.09 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 14 PHE 0.034 0.003 PHE F 19 TYR 0.008 0.001 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 76 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8172 (mtmm) REVERT: B 13 HIS cc_start: 0.6640 (t-90) cc_final: 0.5490 (p-80) REVERT: E 19 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7693 (p90) REVERT: I 28 LYS cc_start: 0.7768 (ptpt) cc_final: 0.5920 (mmtt) outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 0.0959 time to fit residues: 8.3933 Evaluate side-chains 68 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2420 Z= 0.281 Angle : 0.622 4.762 3250 Z= 0.357 Chirality : 0.059 0.257 360 Planarity : 0.002 0.015 420 Dihedral : 8.350 35.271 330 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 4.58 % Allowed : 21.67 % 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: -4.14 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 14 PHE 0.035 0.003 PHE F 19 TYR 0.009 0.001 TYR A 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 77 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8238 (mtmm) REVERT: B 13 HIS cc_start: 0.6687 (t-90) cc_final: 0.5429 (p-80) REVERT: E 19 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7632 (p90) REVERT: I 28 LYS cc_start: 0.7812 (ptpt) cc_final: 0.6028 (mmtt) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.1060 time to fit residues: 9.4515 Evaluate side-chains 70 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU 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 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 HIS I 15 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2420 Z= 0.268 Angle : 0.624 5.147 3250 Z= 0.355 Chirality : 0.060 0.273 360 Planarity : 0.002 0.018 420 Dihedral : 8.393 36.954 330 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 5.42 % Allowed : 20.83 % 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: -4.23 (0.33), 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 0.006 0.001 HIS E 14 PHE 0.024 0.003 PHE G 20 TYR 0.007 0.001 TYR A 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 74 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8243 (mtmm) REVERT: B 13 HIS cc_start: 0.6725 (t-90) cc_final: 0.5491 (p-80) REVERT: E 19 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7594 (p90) REVERT: I 28 LYS cc_start: 0.7831 (ptpt) cc_final: 0.6051 (mmtt) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.0992 time to fit residues: 8.1468 Evaluate side-chains 70 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS 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 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4960 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= 0.223 Angle : 0.612 5.485 3250 Z= 0.343 Chirality : 0.061 0.292 360 Planarity : 0.002 0.021 420 Dihedral : 8.489 41.065 330 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 4.17 % Allowed : 23.33 % 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: -4.27 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 14 PHE 0.028 0.003 PHE G 20 TYR 0.007 0.001 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 72 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8304 (mtmm) REVERT: B 13 HIS cc_start: 0.6577 (t-90) cc_final: 0.5344 (p-80) REVERT: G 19 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7775 (p90) REVERT: I 28 LYS cc_start: 0.7847 (ptpt) cc_final: 0.6059 (mmtt) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1021 time to fit residues: 8.3819 Evaluate side-chains 65 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.004 0.045 2420 Z= 0.244 Angle : 0.629 5.452 3250 Z= 0.354 Chirality : 0.061 0.292 360 Planarity : 0.002 0.017 420 Dihedral : 8.661 42.985 330 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 4.17 % Allowed : 23.33 % 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: -4.25 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.037 0.003 PHE C 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 73 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8315 (mtmm) REVERT: B 13 HIS cc_start: 0.6428 (t-90) cc_final: 0.5259 (p-80) REVERT: I 28 LYS cc_start: 0.7898 (ptpt) cc_final: 0.6112 (mmtt) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.1025 time to fit residues: 8.3369 Evaluate side-chains 69 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS 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 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.0050 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2420 Z= 0.204 Angle : 0.623 5.566 3250 Z= 0.347 Chirality : 0.061 0.288 360 Planarity : 0.002 0.016 420 Dihedral : 8.745 44.905 330 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.67 % Favored : 82.33 % Rotamer: Outliers : 3.33 % Allowed : 24.17 % 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: -4.24 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 14 PHE 0.034 0.003 PHE C 19 TYR 0.008 0.001 TYR E 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 74 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8355 (mtmm) REVERT: E 35 MET cc_start: 0.6625 (ttt) cc_final: 0.6390 (ttt) REVERT: I 28 LYS cc_start: 0.7834 (ptpt) cc_final: 0.6094 (mmtt) outliers start: 8 outliers final: 7 residues processed: 68 average time/residue: 0.1106 time to fit residues: 9.3367 Evaluate side-chains 72 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 14 HIS 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 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.0030 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** 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 = 0.5165 r_free = 0.5165 target = 0.208732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.194397 restraints weight = 2918.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.199337 restraints weight = 1136.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.202471 restraints weight = 584.918| |-----------------------------------------------------------------------------| r_work (final): 0.5140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2420 Z= 0.280 Angle : 0.655 5.609 3250 Z= 0.368 Chirality : 0.060 0.291 360 Planarity : 0.003 0.016 420 Dihedral : 8.778 44.222 330 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 3.33 % Allowed : 25.83 % Favored : 70.83 % 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: -4.19 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 14 PHE 0.037 0.003 PHE C 19 TYR 0.007 0.001 TYR A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1027.76 seconds wall clock time: 19 minutes 22.97 seconds (1162.97 seconds total)