Starting phenix.real_space_refine on Sun Mar 10 14:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/03_2024/7e0f_30931.pdb" } resolution = 3.02 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1248 2.51 5 N 354 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "B" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "C" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "E" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Time building chain proxies: 1.38, per 1000 atoms: 0.68 Number of scatterers: 2022 At special positions: 0 Unit cell: (79.5, 81.62, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 354 7.00 C 1248 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: 0.68 Conformation dependent library (CDL) restraints added in 320.5 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.582A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.344A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.385A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 93 through 94 16 hydrogen bonds defined for protein. 48 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: 0.41 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 378 1.27 - 1.34: 312 1.34 - 1.41: 60 1.41 - 1.47: 366 1.47 - 1.54: 912 Bond restraints: 2028 Sorted by residual: bond pdb=" C GLN C 79 " pdb=" N LYS C 80 " ideal model delta sigma weight residual 1.332 1.269 0.064 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C GLN F 79 " pdb=" N LYS F 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" C GLN D 79 " pdb=" N LYS D 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C GLN B 79 " pdb=" N LYS B 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" C GLN A 79 " pdb=" N LYS A 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.00e+01 ... (remaining 2023 not shown) Histogram of bond angle deviations from ideal: 105.83 - 110.88: 893 110.88 - 115.92: 559 115.92 - 120.97: 654 120.97 - 126.02: 636 126.02 - 131.07: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta sigma weight residual 121.58 115.88 5.70 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1086 17.15 - 34.29: 84 34.29 - 51.43: 12 51.43 - 68.58: 0 68.58 - 85.72: 12 Dihedral angle restraints: 1194 sinusoidal: 390 harmonic: 804 Sorted by residual: dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta harmonic sigma weight residual 180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 1191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 161 0.043 - 0.085: 128 0.085 - 0.127: 54 0.127 - 0.169: 17 0.169 - 0.211: 6 Chirality restraints: 366 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 363 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA A 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA D 90 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 91 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA C 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA C 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 770 2.85 - 3.36: 1787 3.36 - 3.88: 2984 3.88 - 4.39: 3268 4.39 - 4.90: 6828 Nonbonded interactions: 15637 Sorted by model distance: nonbonded pdb=" OG1 THR D 54 " pdb=" OG1 THR D 64 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR E 54 " pdb=" OG1 THR E 64 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR F 54 " pdb=" OG1 THR F 64 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR B 64 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR A 64 " model vdw 2.341 2.440 ... (remaining 15632 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.010 Extract box with map and model: 4.780 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.016 0.086 2028 Z= 1.067 Angle : 0.986 5.709 2748 Z= 0.581 Chirality : 0.069 0.211 366 Planarity : 0.003 0.015 348 Dihedral : 15.885 85.718 678 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % 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: -5.10 (0.40), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.024 0.007 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.220 Fit side-chains REVERT: B 62 GLN cc_start: 0.8853 (pt0) cc_final: 0.8407 (pt0) REVERT: C 62 GLN cc_start: 0.8813 (pt0) cc_final: 0.8532 (pt0) REVERT: C 83 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 60 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7419 (mtpt) REVERT: E 62 GLN cc_start: 0.9017 (pt0) cc_final: 0.8721 (pt0) REVERT: F 61 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8047 (mt-10) REVERT: F 62 GLN cc_start: 0.8878 (pt0) cc_final: 0.8589 (pt0) REVERT: F 83 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7547 (pm20) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1765 time to fit residues: 8.2220 Evaluate side-chains 22 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2028 Z= 0.203 Angle : 0.599 4.610 2748 Z= 0.335 Chirality : 0.052 0.128 366 Planarity : 0.002 0.008 348 Dihedral : 5.473 24.645 288 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.88 % Allowed : 13.73 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.55 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.016 0.004 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.229 Fit side-chains REVERT: A 60 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7888 (mtpt) REVERT: B 62 GLN cc_start: 0.8621 (pt0) cc_final: 0.8274 (pt0) REVERT: C 61 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 83 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7309 (pm20) REVERT: E 60 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7348 (mtpt) REVERT: E 62 GLN cc_start: 0.8775 (pt0) cc_final: 0.8542 (pt0) REVERT: F 61 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 83 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7456 (pm20) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.1046 time to fit residues: 6.3391 Evaluate side-chains 38 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN E 62 GLN F 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2028 Z= 0.228 Angle : 0.571 4.205 2748 Z= 0.321 Chirality : 0.050 0.123 366 Planarity : 0.002 0.010 348 Dihedral : 5.161 23.440 288 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 6.37 % Allowed : 17.65 % Favored : 75.98 % 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: -4.26 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.014 0.004 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.221 Fit side-chains REVERT: B 62 GLN cc_start: 0.8653 (pt0) cc_final: 0.8363 (pt0) REVERT: C 61 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8108 (mt-10) REVERT: C 83 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7251 (pm20) REVERT: D 62 GLN cc_start: 0.8500 (pt0) cc_final: 0.8049 (mt0) REVERT: E 60 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7304 (mtpt) REVERT: E 96 LYS cc_start: 0.8422 (tttm) cc_final: 0.8213 (tttt) REVERT: F 61 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8041 (mt-10) REVERT: F 83 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7431 (pm20) outliers start: 13 outliers final: 11 residues processed: 45 average time/residue: 0.0945 time to fit residues: 5.2458 Evaluate side-chains 39 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2028 Z= 0.297 Angle : 0.579 4.247 2748 Z= 0.328 Chirality : 0.050 0.125 366 Planarity : 0.002 0.018 348 Dihedral : 5.282 23.870 288 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 5.88 % Allowed : 19.12 % 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: -4.03 (0.47), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.017 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.223 Fit side-chains REVERT: B 62 GLN cc_start: 0.8670 (pt0) cc_final: 0.8219 (pt0) REVERT: C 61 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 83 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7271 (pm20) REVERT: E 60 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7324 (mtpt) REVERT: E 96 LYS cc_start: 0.8394 (tttm) cc_final: 0.8168 (tttt) REVERT: F 61 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8066 (mt-10) outliers start: 12 outliers final: 11 residues processed: 39 average time/residue: 0.1021 time to fit residues: 5.0517 Evaluate side-chains 37 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2028 Z= 0.275 Angle : 0.551 4.001 2748 Z= 0.312 Chirality : 0.049 0.125 366 Planarity : 0.002 0.015 348 Dihedral : 5.205 23.543 288 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 7.35 % Allowed : 18.63 % Favored : 74.02 % 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: -3.86 (0.49), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.016 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 28 time to evaluate : 0.229 Fit side-chains REVERT: B 79 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7805 (mm110) REVERT: C 83 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7256 (pm20) REVERT: D 83 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7743 (mm-30) REVERT: E 60 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7314 (mtpt) REVERT: E 79 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7759 (mm110) REVERT: E 96 LYS cc_start: 0.8382 (tttm) cc_final: 0.8163 (tttt) REVERT: F 61 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8123 (mt-10) outliers start: 15 outliers final: 11 residues processed: 41 average time/residue: 0.1097 time to fit residues: 5.4565 Evaluate side-chains 38 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2028 Z= 0.246 Angle : 0.546 4.640 2748 Z= 0.310 Chirality : 0.049 0.125 366 Planarity : 0.002 0.019 348 Dihedral : 5.116 22.838 288 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 7.84 % Allowed : 17.65 % Favored : 74.51 % 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: -3.74 (0.49), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 50 PHE 0.015 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 28 time to evaluate : 0.231 Fit side-chains REVERT: A 96 LYS cc_start: 0.8437 (tttm) cc_final: 0.8194 (tttt) REVERT: B 62 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: B 79 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: C 83 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7249 (pm20) REVERT: D 79 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7956 (mm110) REVERT: D 83 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 62 GLN cc_start: 0.8454 (mt0) cc_final: 0.7634 (mp10) REVERT: E 79 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7769 (mm110) REVERT: E 96 LYS cc_start: 0.8376 (tttm) cc_final: 0.8149 (tttt) REVERT: F 61 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8102 (mt-10) outliers start: 16 outliers final: 11 residues processed: 43 average time/residue: 0.1088 time to fit residues: 5.7103 Evaluate side-chains 42 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2028 Z= 0.121 Angle : 0.486 4.442 2748 Z= 0.274 Chirality : 0.048 0.123 366 Planarity : 0.002 0.016 348 Dihedral : 4.592 19.126 288 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.39 % Allowed : 20.59 % Favored : 74.02 % 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: -3.58 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.011 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.221 Fit side-chains REVERT: B 62 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: D 79 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7938 (mm110) REVERT: D 83 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7659 (mm-30) REVERT: E 62 GLN cc_start: 0.8466 (mt0) cc_final: 0.7725 (pm20) REVERT: E 79 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7697 (mm110) REVERT: F 61 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7910 (mt-10) outliers start: 11 outliers final: 4 residues processed: 42 average time/residue: 0.1260 time to fit residues: 6.3876 Evaluate side-chains 38 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN D 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2028 Z= 0.168 Angle : 0.499 4.807 2748 Z= 0.283 Chirality : 0.048 0.120 366 Planarity : 0.002 0.015 348 Dihedral : 4.656 19.418 288 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.39 % Allowed : 20.59 % Favored : 74.02 % 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: -3.54 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.012 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.253 Fit side-chains REVERT: A 79 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 83 GLU cc_start: 0.7796 (mp0) cc_final: 0.7557 (mm-30) REVERT: B 79 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7810 (mm110) REVERT: D 62 GLN cc_start: 0.8568 (mt0) cc_final: 0.8317 (mt0) REVERT: D 79 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7963 (mm110) REVERT: D 83 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7610 (mm-30) REVERT: E 62 GLN cc_start: 0.8445 (mt0) cc_final: 0.7754 (pm20) REVERT: E 79 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7717 (mm110) REVERT: F 61 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7944 (mt-10) outliers start: 11 outliers final: 4 residues processed: 38 average time/residue: 0.1231 time to fit residues: 5.6539 Evaluate side-chains 37 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2028 Z= 0.160 Angle : 0.475 4.656 2748 Z= 0.270 Chirality : 0.048 0.120 366 Planarity : 0.002 0.018 348 Dihedral : 4.604 18.523 288 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.90 % Allowed : 20.10 % 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: -3.48 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.011 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.344 Fit side-chains REVERT: A 62 GLN cc_start: 0.8602 (pt0) cc_final: 0.8377 (pt0) REVERT: A 79 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: B 79 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7792 (mm110) REVERT: D 62 GLN cc_start: 0.8553 (mt0) cc_final: 0.8025 (mp10) REVERT: D 79 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7978 (mm110) REVERT: D 83 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7629 (mm-30) REVERT: E 62 GLN cc_start: 0.8460 (mt0) cc_final: 0.7787 (pm20) REVERT: E 79 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7710 (mm110) REVERT: F 61 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7977 (mt-10) outliers start: 10 outliers final: 5 residues processed: 36 average time/residue: 0.1153 time to fit residues: 5.0981 Evaluate side-chains 38 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2028 Z= 0.140 Angle : 0.452 4.647 2748 Z= 0.257 Chirality : 0.048 0.121 366 Planarity : 0.002 0.015 348 Dihedral : 4.498 17.553 288 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.43 % Allowed : 21.08 % Favored : 75.49 % 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: -3.40 (0.52), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.012 0.003 PHE E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.211 Fit side-chains REVERT: A 62 GLN cc_start: 0.8437 (pt0) cc_final: 0.7811 (mt0) REVERT: B 79 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7770 (mm110) REVERT: D 62 GLN cc_start: 0.8543 (mt0) cc_final: 0.8105 (mp10) REVERT: D 79 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7925 (mm110) REVERT: E 62 GLN cc_start: 0.8437 (mt0) cc_final: 0.7825 (pm20) REVERT: E 79 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7742 (mm110) REVERT: F 61 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7990 (mt-10) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.1149 time to fit residues: 4.8217 Evaluate side-chains 35 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.0060 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.220723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.159694 restraints weight = 1959.134| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 3.36 r_work: 0.4284 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2028 Z= 0.127 Angle : 0.445 4.537 2748 Z= 0.252 Chirality : 0.048 0.118 366 Planarity : 0.002 0.013 348 Dihedral : 4.332 17.221 288 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.92 % Allowed : 20.59 % Favored : 75.49 % 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: -3.39 (0.52), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.010 0.003 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1022.19 seconds wall clock time: 19 minutes 8.94 seconds (1148.94 seconds total)