Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/03_2024/8bg9_16027_neut.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 6 5.16 5 C 1074 2.51 5 N 300 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "F ASP 7": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.57, per 1000 atoms: 0.93 Number of scatterers: 1692 At special positions: 0 Unit cell: (86.688, 62.608, 30.1, 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 6 16.00 O 312 8.00 N 300 7.00 C 1074 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: 0.74 Conformation dependent library (CDL) restraints added in 316.6 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... No hydrogen bonds 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: 0.00 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: 1.22 - 1.34: 525 1.34 - 1.46: 483 1.46 - 1.58: 708 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1728 Sorted by residual: bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.06e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.04e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER F 8 " pdb=" CB SER F 8 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.78e-02 3.16e+03 3.92e+00 ... (remaining 1723 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.20: 42 107.20 - 113.49: 827 113.49 - 119.78: 611 119.78 - 126.07: 812 126.07 - 132.36: 18 Bond angle restraints: 2310 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" CA TYR E 10 " pdb=" CB TYR E 10 " ideal model delta sigma weight residual 109.72 118.61 -8.89 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR C 10 " pdb=" CA TYR C 10 " pdb=" CB TYR C 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR A 10 " pdb=" CA TYR A 10 " pdb=" CB TYR A 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.63e+01 angle pdb=" CB GLU F 11 " pdb=" CG GLU F 11 " pdb=" CD GLU F 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" CB GLU D 11 " pdb=" CG GLU D 11 " pdb=" CD GLU D 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 ... (remaining 2305 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.61: 780 11.61 - 23.22: 120 23.22 - 34.82: 42 34.82 - 46.43: 9 46.43 - 58.03: 9 Dihedral angle restraints: 960 sinusoidal: 366 harmonic: 594 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER B 8 " pdb=" C SER B 8 " pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 957 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.045: 87 0.045 - 0.087: 62 0.087 - 0.129: 46 0.129 - 0.171: 24 0.171 - 0.213: 15 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL C 18 " pdb=" N VAL C 18 " pdb=" C VAL C 18 " pdb=" CB VAL C 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 18 " pdb=" N VAL A 18 " pdb=" C VAL A 18 " pdb=" CB VAL A 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 231 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C SER D 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER D 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY D 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C SER B 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY B 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 8 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.58e+00 pdb=" C SER F 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY F 9 " 0.009 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 809 2.97 - 3.45: 1558 3.45 - 3.93: 2520 3.93 - 4.42: 2733 4.42 - 4.90: 4413 Nonbonded interactions: 12033 Sorted by model distance: nonbonded pdb=" OD1 ASP B 7 " pdb=" N GLY B 9 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP A 7 " pdb=" N GLY A 9 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP D 7 " pdb=" N GLY D 9 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP E 7 " pdb=" N GLY E 9 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP C 7 " pdb=" N GLY C 9 " model vdw 2.485 2.520 ... (remaining 12028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.680 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.540 Find NCS groups from input model: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.008 0.037 1728 Z= 0.474 Angle : 1.465 8.889 2310 Z= 0.953 Chirality : 0.091 0.213 234 Planarity : 0.007 0.043 306 Dihedral : 14.959 58.032 588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Rotamer: Outliers : 12.50 % Allowed : 23.21 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 6 PHE 0.025 0.006 PHE E 19 TYR 0.020 0.005 TYR D 10 ARG 0.006 0.002 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 35 time to evaluate : 0.222 Fit side-chains REVERT: A 10 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 10 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.6877 (t80) REVERT: C 3 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6864 (tt0) REVERT: C 5 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7350 (ttm110) REVERT: C 10 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6332 (t80) REVERT: D 5 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7383 (mtp180) REVERT: D 10 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6182 (t80) outliers start: 21 outliers final: 11 residues processed: 55 average time/residue: 0.1185 time to fit residues: 7.5052 Evaluate side-chains 42 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 15 GLN B 13 HIS C 13 HIS C 14 HIS D 13 HIS D 14 HIS E 13 HIS E 15 GLN F 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 1728 Z= 0.243 Angle : 0.783 7.410 2310 Z= 0.413 Chirality : 0.056 0.154 234 Planarity : 0.003 0.011 306 Dihedral : 10.700 49.159 257 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 10.71 % Allowed : 15.48 % 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: -5.24 (0.28), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.21), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.011 0.002 PHE B 4 TYR 0.023 0.004 TYR B 10 ARG 0.002 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 22 time to evaluate : 0.201 Fit side-chains REVERT: C 5 ARG cc_start: 0.8439 (ttm170) cc_final: 0.7987 (ttm110) REVERT: D 8 SER cc_start: 0.8863 (m) cc_final: 0.8445 (t) outliers start: 18 outliers final: 13 residues processed: 39 average time/residue: 0.1256 time to fit residues: 5.7915 Evaluate side-chains 33 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 20 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1728 Z= 0.111 Angle : 0.555 5.314 2310 Z= 0.291 Chirality : 0.049 0.138 234 Planarity : 0.002 0.007 306 Dihedral : 7.855 55.892 239 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.76 % Allowed : 20.83 % Favored : 74.40 % 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: -4.37 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.006 0.001 PHE D 4 TYR 0.018 0.003 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.203 Fit side-chains REVERT: C 5 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7817 (ttm110) REVERT: D 5 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7807 (mmm-85) REVERT: D 8 SER cc_start: 0.8830 (m) cc_final: 0.8519 (t) outliers start: 8 outliers final: 7 residues processed: 26 average time/residue: 0.1333 time to fit residues: 4.1514 Evaluate side-chains 26 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 1728 Z= 0.181 Angle : 0.602 5.511 2310 Z= 0.316 Chirality : 0.049 0.132 234 Planarity : 0.002 0.011 306 Dihedral : 7.637 55.412 234 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 11.31 % Allowed : 14.88 % 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: -4.24 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.28), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.010 0.002 PHE D 20 TYR 0.023 0.004 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 18 time to evaluate : 0.208 Fit side-chains REVERT: C 1 ASP cc_start: 0.5115 (OUTLIER) cc_final: 0.4248 (t0) REVERT: C 5 ARG cc_start: 0.8534 (ttm170) cc_final: 0.8309 (ttm170) REVERT: D 8 SER cc_start: 0.9148 (m) cc_final: 0.8736 (t) REVERT: D 23 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8504 (m-30) REVERT: E 1 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8062 (t0) outliers start: 19 outliers final: 16 residues processed: 33 average time/residue: 0.0907 time to fit residues: 3.7510 Evaluate side-chains 36 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 17 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1728 Z= 0.108 Angle : 0.494 5.240 2310 Z= 0.258 Chirality : 0.047 0.124 234 Planarity : 0.001 0.006 306 Dihedral : 7.442 57.674 234 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.55 % Allowed : 22.02 % Favored : 71.43 % 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: -3.88 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.006 0.001 PHE D 20 TYR 0.016 0.003 TYR B 10 ARG 0.000 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 20 time to evaluate : 0.201 Fit side-chains REVERT: C 5 ARG cc_start: 0.8515 (ttm170) cc_final: 0.7732 (mtp180) REVERT: D 8 SER cc_start: 0.8964 (m) cc_final: 0.8675 (t) outliers start: 11 outliers final: 10 residues processed: 30 average time/residue: 0.0954 time to fit residues: 3.5978 Evaluate side-chains 27 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 17 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain F residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1728 Z= 0.222 Angle : 0.653 6.879 2310 Z= 0.336 Chirality : 0.051 0.150 234 Planarity : 0.003 0.011 306 Dihedral : 7.954 56.403 234 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 10.71 % Allowed : 17.86 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.011 0.002 PHE E 4 TYR 0.025 0.005 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 19 time to evaluate : 0.206 Fit side-chains REVERT: A 1 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6004 (t0) REVERT: A 3 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7776 (tt0) REVERT: B 5 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8130 (tpp80) REVERT: C 1 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.4340 (t0) REVERT: D 8 SER cc_start: 0.9184 (m) cc_final: 0.8763 (t) REVERT: E 10 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7025 (p90) REVERT: F 1 ASP cc_start: 0.8098 (p0) cc_final: 0.7876 (p0) outliers start: 18 outliers final: 13 residues processed: 35 average time/residue: 0.0917 time to fit residues: 4.0073 Evaluate side-chains 35 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 19 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1728 Z= 0.193 Angle : 0.602 7.454 2310 Z= 0.312 Chirality : 0.050 0.135 234 Planarity : 0.002 0.009 306 Dihedral : 8.008 57.259 234 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 10.12 % Allowed : 17.26 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.009 0.002 PHE C 4 TYR 0.021 0.004 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 21 time to evaluate : 0.200 Fit side-chains REVERT: A 1 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6102 (t0) REVERT: A 3 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7788 (tt0) REVERT: B 5 ARG cc_start: 0.8492 (ttt180) cc_final: 0.8217 (tpp80) REVERT: D 8 SER cc_start: 0.9111 (m) cc_final: 0.8654 (t) REVERT: E 10 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7141 (p90) REVERT: F 1 ASP cc_start: 0.8148 (p0) cc_final: 0.7922 (p0) outliers start: 17 outliers final: 14 residues processed: 36 average time/residue: 0.0944 time to fit residues: 4.2250 Evaluate side-chains 36 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1728 Z= 0.115 Angle : 0.510 5.797 2310 Z= 0.264 Chirality : 0.047 0.123 234 Planarity : 0.001 0.006 306 Dihedral : 7.733 58.347 234 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 9.52 % Allowed : 17.26 % Favored : 73.21 % 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: -3.97 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.006 0.001 PHE C 4 TYR 0.016 0.003 TYR B 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 23 time to evaluate : 0.211 Fit side-chains REVERT: A 1 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.5768 (t0) REVERT: A 3 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7768 (tt0) REVERT: B 3 GLU cc_start: 0.8001 (tt0) cc_final: 0.7771 (tt0) REVERT: B 5 ARG cc_start: 0.8443 (ttt180) cc_final: 0.8174 (tpp80) REVERT: D 8 SER cc_start: 0.9067 (m) cc_final: 0.8844 (t) REVERT: E 10 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7287 (p90) REVERT: F 1 ASP cc_start: 0.8237 (p0) cc_final: 0.7958 (p0) outliers start: 16 outliers final: 14 residues processed: 37 average time/residue: 0.0934 time to fit residues: 4.2972 Evaluate side-chains 37 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 21 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1728 Z= 0.239 Angle : 0.649 7.712 2310 Z= 0.337 Chirality : 0.051 0.135 234 Planarity : 0.003 0.010 306 Dihedral : 8.212 56.577 234 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 10.12 % Allowed : 16.67 % Favored : 73.21 % 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: -4.20 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.011 0.002 PHE E 4 TYR 0.024 0.004 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 20 time to evaluate : 0.147 Fit side-chains REVERT: A 1 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.5823 (t0) REVERT: A 3 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7758 (tt0) REVERT: B 5 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8263 (tpp80) REVERT: D 8 SER cc_start: 0.9193 (m) cc_final: 0.8723 (t) REVERT: E 10 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7027 (p90) REVERT: F 1 ASP cc_start: 0.8104 (p0) cc_final: 0.7833 (p0) outliers start: 17 outliers final: 14 residues processed: 34 average time/residue: 0.0673 time to fit residues: 2.8880 Evaluate side-chains 36 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1728 Z= 0.164 Angle : 0.592 7.147 2310 Z= 0.300 Chirality : 0.048 0.130 234 Planarity : 0.002 0.008 306 Dihedral : 8.073 58.465 234 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 9.52 % Allowed : 16.67 % 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: -4.07 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 13 PHE 0.008 0.001 PHE D 20 TYR 0.019 0.004 TYR B 10 ARG 0.001 0.000 ARG A 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.208 Fit side-chains REVERT: A 1 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.5860 (t0) REVERT: A 3 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7763 (tt0) REVERT: B 5 ARG cc_start: 0.8539 (ttt180) cc_final: 0.8262 (tpp80) REVERT: D 8 SER cc_start: 0.9140 (m) cc_final: 0.8758 (t) REVERT: E 10 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7148 (p90) REVERT: F 1 ASP cc_start: 0.8160 (p0) cc_final: 0.7839 (p0) outliers start: 16 outliers final: 14 residues processed: 34 average time/residue: 0.0942 time to fit residues: 3.9986 Evaluate side-chains 36 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 0.0470 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.340223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5557 r_free = 0.5557 target = 0.280215 restraints weight = 2270.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5572 r_free = 0.5572 target = 0.282499 restraints weight = 1086.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.283802 restraints weight = 620.839| |-----------------------------------------------------------------------------| r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.7752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1728 Z= 0.106 Angle : 0.509 5.368 2310 Z= 0.259 Chirality : 0.046 0.120 234 Planarity : 0.001 0.006 306 Dihedral : 7.833 59.941 234 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 8.93 % Allowed : 17.26 % 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: -3.81 (0.44), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.34), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.005 0.001 PHE B 19 TYR 0.015 0.003 TYR B 10 ARG 0.001 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 847.32 seconds wall clock time: 16 minutes 13.93 seconds (973.93 seconds total)