Starting phenix.real_space_refine on Sun Mar 10 14:59:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot3_17167/03_2024/8ot3_17167.pdb" } resolution = 2.73 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1596 2.51 5 N 432 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2460 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "G" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "H" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "K" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Time building chain proxies: 1.60, per 1000 atoms: 0.65 Number of scatterers: 2460 At special positions: 0 Unit cell: (92.466, 73.786, 42.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.73 Conformation dependent library (CDL) restraints added in 469.7 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 17 " --> pdb=" O VAL K 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP C 23 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP E 23 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP G 23 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP I 23 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP K 23 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 17 " --> pdb=" O VAL L 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP D 23 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP F 23 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP H 23 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP J 23 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP L 23 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 32 30 hydrogen bonds defined for protein. 90 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: 0.55 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 408 1.29 - 1.42: 612 1.42 - 1.55: 1452 1.55 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" C ILE K 32 " pdb=" O ILE K 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE G 32 " pdb=" O ILE G 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE D 32 " pdb=" O ILE D 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE L 32 " pdb=" O ILE L 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE J 32 " pdb=" O ILE J 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 100.47 - 106.86: 132 106.86 - 113.25: 1200 113.25 - 119.64: 956 119.64 - 126.04: 1024 126.04 - 132.43: 24 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY I 38 " pdb=" C GLY I 38 " pdb=" O GLY I 38 " ideal model delta sigma weight residual 122.23 118.44 3.79 6.90e-01 2.10e+00 3.02e+01 angle pdb=" CA GLY B 38 " pdb=" C GLY B 38 " pdb=" O GLY B 38 " ideal model delta sigma weight residual 122.23 118.47 3.76 6.90e-01 2.10e+00 2.96e+01 angle pdb=" CA GLY A 38 " pdb=" C GLY A 38 " pdb=" O GLY A 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY J 38 " pdb=" C GLY J 38 " pdb=" O GLY J 38 " ideal model delta sigma weight residual 122.23 118.49 3.74 6.90e-01 2.10e+00 2.94e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1272 16.52 - 33.03: 72 33.03 - 49.55: 36 49.55 - 66.07: 0 66.07 - 82.58: 12 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA ILE F 32 " pdb=" CB ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CD1 ILE F 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE L 32 " pdb=" CB ILE L 32 " pdb=" CG1 ILE L 32 " pdb=" CD1 ILE L 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE J 32 " pdb=" CB ILE J 32 " pdb=" CG1 ILE J 32 " pdb=" CD1 ILE J 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.47 48.53 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 60 0.045 - 0.091: 72 0.091 - 0.136: 108 0.136 - 0.181: 65 0.181 - 0.227: 79 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE I 32 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE I 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE C 32 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE C 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 32 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE H 32 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE H 32 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY H 33 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1370 3.03 - 3.50: 2330 3.50 - 3.96: 3720 3.96 - 4.43: 4345 4.43 - 4.90: 8804 Nonbonded interactions: 20569 Sorted by model distance: nonbonded pdb=" N VAL B 36 " pdb=" O VAL B 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL D 36 " pdb=" O VAL D 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL A 36 " pdb=" O VAL A 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL L 36 " pdb=" O VAL L 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL I 36 " pdb=" O VAL I 36 " model vdw 2.559 2.496 ... (remaining 20564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.580 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: 2.810 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:15.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.014 0.075 2496 Z= 0.948 Angle : 2.331 9.747 3336 Z= 1.679 Chirality : 0.131 0.227 384 Planarity : 0.010 0.032 420 Dihedral : 16.882 82.580 840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -3.27 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 14 PHE 0.008 0.002 PHE K 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5308 time to fit residues: 52.1526 Evaluate side-chains 88 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS E 14 HIS G 14 HIS I 14 HIS J 14 HIS K 14 HIS L 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.193 Angle : 0.700 7.943 3336 Z= 0.376 Chirality : 0.051 0.112 384 Planarity : 0.002 0.013 420 Dihedral : 4.040 10.180 324 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 21.43 % Favored : 73.81 % 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: -3.93 (0.25), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS C 14 PHE 0.012 0.002 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.240 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 0.6637 time to fit residues: 39.3264 Evaluate side-chains 51 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS G 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2496 Z= 0.152 Angle : 0.579 6.597 3336 Z= 0.306 Chirality : 0.051 0.123 384 Planarity : 0.002 0.011 420 Dihedral : 3.794 10.131 324 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 23.02 % Favored : 73.81 % 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 (0.25), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 14 PHE 0.011 0.002 PHE G 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.287 Fit side-chains outliers start: 8 outliers final: 9 residues processed: 50 average time/residue: 0.7296 time to fit residues: 37.9139 Evaluate side-chains 56 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2496 Z= 0.160 Angle : 0.569 5.670 3336 Z= 0.298 Chirality : 0.050 0.121 384 Planarity : 0.002 0.008 420 Dihedral : 3.839 9.321 324 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.37 % Allowed : 21.03 % Favored : 74.60 % 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 (0.25), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 14 PHE 0.010 0.002 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.273 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.7514 time to fit residues: 35.8858 Evaluate side-chains 49 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2496 Z= 0.154 Angle : 0.553 4.881 3336 Z= 0.289 Chirality : 0.050 0.120 384 Planarity : 0.001 0.009 420 Dihedral : 3.799 9.500 324 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 21.43 % Favored : 75.40 % 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 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 14 PHE 0.009 0.002 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.267 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 44 average time/residue: 0.8126 time to fit residues: 37.0396 Evaluate side-chains 50 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2496 Z= 0.196 Angle : 0.589 4.799 3336 Z= 0.309 Chirality : 0.050 0.129 384 Planarity : 0.002 0.014 420 Dihedral : 3.959 8.869 324 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 22.22 % Favored : 74.21 % 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: -3.41 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.011 0.002 PHE I 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.252 Fit side-chains REVERT: A 35 MET cc_start: 0.6695 (mtt) cc_final: 0.6459 (mtt) outliers start: 9 outliers final: 9 residues processed: 42 average time/residue: 0.8022 time to fit residues: 34.9006 Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2496 Z= 0.215 Angle : 0.618 5.151 3336 Z= 0.325 Chirality : 0.050 0.124 384 Planarity : 0.002 0.017 420 Dihedral : 4.094 9.090 324 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 22.22 % Favored : 74.21 % 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: -3.35 (0.29), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 14 PHE 0.011 0.002 PHE I 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.280 Fit side-chains REVERT: A 35 MET cc_start: 0.6769 (mtt) cc_final: 0.6567 (mtt) REVERT: L 13 HIS cc_start: 0.6804 (m90) cc_final: 0.6281 (m90) outliers start: 9 outliers final: 9 residues processed: 44 average time/residue: 0.9450 time to fit residues: 42.9094 Evaluate side-chains 46 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2496 Z= 0.172 Angle : 0.623 6.128 3336 Z= 0.326 Chirality : 0.050 0.123 384 Planarity : 0.002 0.020 420 Dihedral : 3.925 9.709 324 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 23.41 % Favored : 73.81 % 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: -3.24 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 14 PHE 0.008 0.001 PHE I 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.277 Fit side-chains REVERT: A 35 MET cc_start: 0.6693 (mtt) cc_final: 0.6464 (mtt) outliers start: 7 outliers final: 7 residues processed: 43 average time/residue: 1.0011 time to fit residues: 44.3636 Evaluate side-chains 46 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER 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: 4.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2496 Z= 0.297 Angle : 0.720 6.309 3336 Z= 0.379 Chirality : 0.050 0.126 384 Planarity : 0.003 0.025 420 Dihedral : 4.326 9.582 324 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 22.62 % Favored : 73.81 % 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: -3.52 (0.30), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 14 PHE 0.013 0.002 PHE I 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.283 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 43 average time/residue: 0.9482 time to fit residues: 42.0405 Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2496 Z= 0.233 Angle : 0.734 7.582 3336 Z= 0.384 Chirality : 0.051 0.124 384 Planarity : 0.003 0.027 420 Dihedral : 4.178 9.159 324 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 23.41 % Favored : 73.41 % 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: -3.50 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 14 PHE 0.010 0.002 PHE I 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.286 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 44 average time/residue: 0.9110 time to fit residues: 41.4013 Evaluate side-chains 50 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER 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: 0.8980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.134888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.117243 restraints weight = 3458.280| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.54 r_work: 0.4115 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2496 Z= 0.259 Angle : 0.771 7.352 3336 Z= 0.403 Chirality : 0.051 0.125 384 Planarity : 0.003 0.029 420 Dihedral : 4.247 9.608 324 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 23.02 % Favored : 73.41 % 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: -3.57 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 14 PHE 0.011 0.002 PHE I 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.10 seconds wall clock time: 26 minutes 1.37 seconds (1561.37 seconds total)