Starting phenix.real_space_refine on Thu Dec 7 16:11:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff3_29037/12_2023/8ff3_29037.pdb" } resolution = 3.09 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= 0.003 sd= 0.041 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 696 2.51 5 N 174 2.21 5 O 192 1.98 5 H 1122 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2190 Number of models: 1 Model: "" Number of chains: 6 Chain: "b" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "a" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "c" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 365 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 1.42, per 1000 atoms: 0.65 Number of scatterers: 2190 At special positions: 0 Unit cell: (39.2, 84, 30.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 192 8.00 N 174 7.00 C 696 6.00 H 1122 1.00 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: 1.86 Conformation dependent library (CDL) restraints added in 292.1 milliseconds 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 240 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'a' and resid 16 through 24 removed outlier: 6.870A pdb=" N VAL b 24 " --> pdb=" O ASP a 23 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU b 17 " --> pdb=" O VAL c 18 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N PHE c 20 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE b 19 " --> pdb=" O PHE c 20 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLU c 22 " --> pdb=" O PHE b 19 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA b 21 " --> pdb=" O GLU c 22 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL c 24 " --> pdb=" O ALA b 21 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP b 23 " --> pdb=" O VAL c 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 27 through 28 removed outlier: 5.583A pdb=" N ASN b 27 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 31 through 36 removed outlier: 6.796A pdb=" N LEU b 34 " --> pdb=" O GLY a 33 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET a 35 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL b 36 " --> pdb=" O MET a 35 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE b 31 " --> pdb=" O ILE c 32 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU c 34 " --> pdb=" O ILE b 31 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY b 33 " --> pdb=" O LEU c 34 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N VAL c 36 " --> pdb=" O GLY b 33 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N MET b 35 " --> pdb=" O VAL c 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 16 through 24 removed outlier: 6.815A pdb=" N VAL C 24 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 17 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE B 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 19 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU B 22 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA A 21 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP A 23 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 32 removed outlier: 6.467A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.454A pdb=" N MET C 35 " --> pdb=" O VAL B 36 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.67 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1122 1.03 - 1.23: 0 1.23 - 1.42: 420 1.42 - 1.61: 642 1.61 - 1.80: 12 Bond restraints: 2196 Sorted by residual: bond pdb=" CB MET A 35 " pdb=" CG MET A 35 " ideal model delta sigma weight residual 1.520 1.507 0.013 3.00e-02 1.11e+03 1.93e-01 bond pdb=" CB MET B 35 " pdb=" CG MET B 35 " ideal model delta sigma weight residual 1.520 1.508 0.012 3.00e-02 1.11e+03 1.73e-01 bond pdb=" CB MET C 35 " pdb=" CG MET C 35 " ideal model delta sigma weight residual 1.520 1.508 0.012 3.00e-02 1.11e+03 1.62e-01 bond pdb=" C LYS b 28 " pdb=" N GLY b 29 " ideal model delta sigma weight residual 1.329 1.323 0.006 1.57e-02 4.06e+03 1.42e-01 bond pdb=" CA VAL c 24 " pdb=" C VAL c 24 " ideal model delta sigma weight residual 1.525 1.521 0.004 1.17e-02 7.31e+03 1.23e-01 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 100.91 - 105.78: 6 105.78 - 110.66: 2407 110.66 - 115.53: 535 115.53 - 120.40: 441 120.40 - 125.28: 595 Bond angle restraints: 3984 Sorted by residual: angle pdb=" N LYS c 28 " pdb=" CA LYS c 28 " pdb=" C LYS c 28 " ideal model delta sigma weight residual 108.76 106.74 2.02 1.69e+00 3.50e-01 1.43e+00 angle pdb=" N ALA a 30 " pdb=" CA ALA a 30 " pdb=" C ALA a 30 " ideal model delta sigma weight residual 109.24 111.11 -1.87 1.63e+00 3.76e-01 1.32e+00 angle pdb=" N LYS b 28 " pdb=" CA LYS b 28 " pdb=" C LYS b 28 " ideal model delta sigma weight residual 108.76 106.84 1.92 1.69e+00 3.50e-01 1.29e+00 angle pdb=" C LYS b 28 " pdb=" CA LYS b 28 " pdb=" CB LYS b 28 " ideal model delta sigma weight residual 109.70 111.70 -2.00 1.81e+00 3.05e-01 1.22e+00 angle pdb=" N ALA c 30 " pdb=" CA ALA c 30 " pdb=" C ALA c 30 " ideal model delta sigma weight residual 109.24 111.02 -1.78 1.63e+00 3.76e-01 1.19e+00 ... (remaining 3979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.77: 800 9.77 - 19.54: 77 19.54 - 29.31: 29 29.31 - 39.08: 9 39.08 - 48.85: 15 Dihedral angle restraints: 930 sinusoidal: 486 harmonic: 444 Sorted by residual: dihedral pdb=" CA PHE b 19 " pdb=" C PHE b 19 " pdb=" N PHE b 20 " pdb=" CA PHE b 20 " ideal model delta harmonic sigma weight residual 180.00 -165.07 -14.93 0 5.00e+00 4.00e-02 8.91e+00 dihedral pdb=" CA PHE a 19 " pdb=" C PHE a 19 " pdb=" N PHE a 20 " pdb=" CA PHE a 20 " ideal model delta harmonic sigma weight residual -180.00 -165.44 -14.56 0 5.00e+00 4.00e-02 8.48e+00 dihedral pdb=" CA LYS a 28 " pdb=" C LYS a 28 " pdb=" N GLY a 29 " pdb=" CA GLY a 29 " ideal model delta harmonic sigma weight residual -180.00 -165.90 -14.10 0 5.00e+00 4.00e-02 7.95e+00 ... (remaining 927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 86 0.027 - 0.054: 42 0.054 - 0.082: 4 0.082 - 0.109: 18 0.109 - 0.136: 18 Chirality restraints: 168 Sorted by residual: 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 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 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 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 165 not shown) Planarity restraints: 324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE b 20 " -0.006 2.00e-02 2.50e+03 3.22e-03 3.11e-01 pdb=" CG PHE b 20 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE b 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE b 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE b 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE b 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE b 20 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE b 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE b 20 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE b 20 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE b 20 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE b 20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 20 " -0.005 2.00e-02 2.50e+03 2.41e-03 1.74e-01 pdb=" CG PHE a 20 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE a 20 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE a 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE a 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE a 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE a 20 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE a 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE a 20 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE a 20 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE a 20 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE a 20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS b 28 " 0.002 2.00e-02 2.50e+03 3.74e-03 1.40e-01 pdb=" C LYS b 28 " -0.006 2.00e-02 2.50e+03 pdb=" O LYS b 28 " 0.002 2.00e-02 2.50e+03 pdb=" N GLY b 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 321 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 906 2.40 - 2.95: 4991 2.95 - 3.50: 5036 3.50 - 4.05: 7239 4.05 - 4.60: 10453 Nonbonded interactions: 28625 Sorted by model distance: nonbonded pdb=" OD1 ASN b 27 " pdb="HD21 ASN a 27 " model vdw 1.846 1.850 nonbonded pdb=" O ASN A 27 " pdb=" H LYS B 28 " model vdw 1.991 1.850 nonbonded pdb=" O PHE b 19 " pdb=" H PHE c 20 " model vdw 2.000 1.850 nonbonded pdb=" O ASN b 27 " pdb=" H LYS c 28 " model vdw 2.028 1.850 nonbonded pdb=" H LYS C 28 " pdb=" O ASN B 27 " model vdw 2.034 1.850 ... (remaining 28620 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 'a' selection = chain 'b' selection = chain 'c' } 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: 0.730 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: 0.040 Extract box with map and model: 3.010 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 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 : 0.002 0.013 1074 Z= 0.140 Angle : 0.433 2.114 1428 Z= 0.245 Chirality : 0.056 0.136 168 Planarity : 0.001 0.004 180 Dihedral : 8.698 45.499 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -2.15 (0.52), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE b 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.3453 time to fit residues: 10.9071 Evaluate side-chains 28 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.6485 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1074 Z= 0.105 Angle : 0.419 2.897 1428 Z= 0.232 Chirality : 0.056 0.135 168 Planarity : 0.001 0.007 180 Dihedral : 5.033 15.022 144 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % 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: -2.18 (0.53), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.41), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3342 time to fit residues: 9.8438 Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 1 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: 0.6560 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1074 Z= 0.218 Angle : 0.453 2.812 1428 Z= 0.253 Chirality : 0.053 0.139 168 Planarity : 0.001 0.006 180 Dihedral : 5.526 16.943 144 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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: -2.20 (0.53), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.41), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE b 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3331 time to fit residues: 9.4504 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.6549 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1074 Z= 0.170 Angle : 0.424 3.140 1428 Z= 0.233 Chirality : 0.054 0.134 168 Planarity : 0.001 0.005 180 Dihedral : 5.257 16.082 144 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.93 % Allowed : 12.04 % Favored : 87.04 % 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: -2.24 (0.54), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.41), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.176 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.3695 time to fit residues: 10.4095 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0380 time to fit residues: 0.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6532 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1074 Z= 0.121 Angle : 0.395 3.126 1428 Z= 0.213 Chirality : 0.055 0.136 168 Planarity : 0.001 0.005 180 Dihedral : 4.907 14.781 144 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.17 (0.55), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.42), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.183 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3347 time to fit residues: 9.4876 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1074 Z= 0.162 Angle : 0.409 3.487 1428 Z= 0.220 Chirality : 0.054 0.135 168 Planarity : 0.001 0.005 180 Dihedral : 4.911 15.268 144 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.18 (0.56), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.42), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.171 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.3532 time to fit residues: 9.6158 Evaluate side-chains 25 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.6547 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1074 Z= 0.133 Angle : 0.390 3.259 1428 Z= 0.209 Chirality : 0.055 0.134 168 Planarity : 0.001 0.005 180 Dihedral : 4.692 14.941 144 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.15 (0.57), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.164 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3348 time to fit residues: 9.5634 Evaluate side-chains 26 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4712 ------------------------------------------------------------------------------- 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: 0.6525 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 1074 Z= 0.096 Angle : 0.373 3.289 1428 Z= 0.199 Chirality : 0.055 0.135 168 Planarity : 0.001 0.003 180 Dihedral : 4.418 14.542 144 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.13 (0.58), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.45), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.183 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3285 time to fit residues: 9.7225 Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6549 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1074 Z= 0.129 Angle : 0.386 3.535 1428 Z= 0.207 Chirality : 0.054 0.131 168 Planarity : 0.001 0.004 180 Dihedral : 4.427 15.136 144 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.10 (0.60), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE a 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.3262 time to fit residues: 10.0001 Evaluate side-chains 28 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6556 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1074 Z= 0.137 Angle : 0.387 3.494 1428 Z= 0.207 Chirality : 0.054 0.128 168 Planarity : 0.001 0.004 180 Dihedral : 4.408 15.244 144 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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: -2.13 (0.60), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE a 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.196 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3274 time to fit residues: 9.6987 Evaluate side-chains 27 residues out of total 108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.143031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132370 restraints weight = 4568.866| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.74 r_work: 0.4036 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1074 Z= 0.134 Angle : 0.383 3.434 1428 Z= 0.205 Chirality : 0.054 0.127 168 Planarity : 0.001 0.004 180 Dihedral : 4.349 15.076 144 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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: -2.14 (0.60), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE a 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.52 seconds wall clock time: 34 minutes 12.75 seconds (2052.75 seconds total)