Starting phenix.real_space_refine (version: dev) on Thu Feb 16 20:19:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/02_2023/7e0f_30931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/02_2023/7e0f_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_30931/02_2023/7e0f_30931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/02_2023/7e0f_30931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/02_2023/7e0f_30931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e0f_30931/02_2023/7e0f_30931.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 1.64, per 1000 atoms: 0.81 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: 0.87 Conformation dependent library (CDL) restraints added in 354.4 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: 0.16 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: 0.39 Time building geometry restraints manager: 0.93 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 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. 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: 1.240 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: 4.810 Check model and map are aligned: 0.030 Process input model: 11.050 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 % 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 *********************** 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 : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1736 time to fit residues: 8.0799 Evaluate side-chains 21 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2752 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.7980 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 2028 Z= 0.195 Angle : 0.601 4.697 2748 Z= 0.335 Chirality : 0.051 0.127 366 Planarity : 0.002 0.009 348 Dihedral : 5.452 24.518 288 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 5.39 % 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: -4.54 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.34), residues: 282 *********************** 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 49 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.223 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1019 time to fit residues: 6.0676 Evaluate side-chains 36 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0225 time to fit residues: 0.6351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 2028 Z= 0.358 Angle : 0.635 4.470 2748 Z= 0.359 Chirality : 0.052 0.126 366 Planarity : 0.002 0.008 348 Dihedral : 5.555 25.493 288 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 2.94 % 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: -4.37 (0.45), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.34), residues: 282 *********************** 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 34 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.223 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.1034 time to fit residues: 4.1416 Evaluate side-chains 30 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0214 time to fit residues: 0.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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** D 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2534 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= 0.130 Angle : 0.488 3.850 2748 Z= 0.274 Chirality : 0.048 0.122 366 Planarity : 0.002 0.020 348 Dihedral : 4.653 20.033 288 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.49 % 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: -3.95 (0.48), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.37), residues: 282 *********************** 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 36 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.250 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1235 time to fit residues: 5.2637 Evaluate side-chains 27 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2028 Z= 0.200 Angle : 0.529 4.549 2748 Z= 0.301 Chirality : 0.049 0.122 366 Planarity : 0.002 0.018 348 Dihedral : 4.786 21.330 288 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 1.47 % 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: -3.72 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.38), residues: 282 *********************** 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 30 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.1175 time to fit residues: 4.0236 Evaluate side-chains 27 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.231 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0466 time to fit residues: 0.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.012 2028 Z= 0.146 Angle : 0.480 4.275 2748 Z= 0.272 Chirality : 0.048 0.121 366 Planarity : 0.002 0.015 348 Dihedral : 4.528 19.565 288 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.47 % 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: -3.63 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.39), residues: 282 *********************** 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 30 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.236 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.1416 time to fit residues: 4.9414 Evaluate side-chains 25 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0503 time to fit residues: 0.3684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 62 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2028 Z= 0.196 Angle : 0.502 4.838 2748 Z= 0.286 Chirality : 0.049 0.143 366 Planarity : 0.002 0.017 348 Dihedral : 4.644 20.093 288 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.98 % 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: -3.61 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.39), residues: 282 *********************** 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 28 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.231 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1400 time to fit residues: 4.6278 Evaluate side-chains 25 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0516 time to fit residues: 0.3831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2028 Z= 0.226 Angle : 0.509 4.555 2748 Z= 0.291 Chirality : 0.049 0.122 366 Planarity : 0.002 0.010 348 Dihedral : 4.846 20.835 288 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 2.45 % 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: -3.61 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.39), residues: 282 *********************** 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 28 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.234 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.0950 time to fit residues: 3.3858 Evaluate side-chains 27 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0275 time to fit residues: 0.4706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN D 79 GLN E 62 GLN E 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 2028 Z= 0.099 Angle : 0.441 4.236 2748 Z= 0.249 Chirality : 0.048 0.117 366 Planarity : 0.002 0.011 348 Dihedral : 4.274 16.591 288 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.47 % 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: -3.49 (0.51), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.39), residues: 282 *********************** 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 33 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.204 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1172 time to fit residues: 4.5957 Evaluate side-chains 26 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0470 time to fit residues: 0.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2028 Z= 0.144 Angle : 0.485 4.998 2748 Z= 0.274 Chirality : 0.048 0.119 366 Planarity : 0.001 0.006 348 Dihedral : 4.343 17.498 288 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.00 % 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: -3.39 (0.52), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.39), residues: 282 ********************** 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 28 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1569 time to fit residues: 5.2368 Evaluate side-chains 23 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4889 r_free = 0.4889 target = 0.212676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.151984 restraints weight = 1989.735| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.29 r_work: 0.4196 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 2028 Z= 0.243 Angle : 0.531 4.355 2748 Z= 0.305 Chirality : 0.050 0.145 366 Planarity : 0.002 0.018 348 Dihedral : 4.749 21.509 288 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.49 % 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 : -2.58 (0.39), residues: 282 =============================================================================== Job complete usr+sys time: 962.88 seconds wall clock time: 17 minutes 57.38 seconds (1077.38 seconds total)