Starting phenix.real_space_refine on Wed Nov 13 22:53:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2024/8bg9_16027_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_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_16027/11_2024/8bg9_16027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2024/8bg9_16027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2024/8bg9_16027_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2024/8bg9_16027_neut.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.25, per 1000 atoms: 1.33 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 - 3.00 Amino acid : True - 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: 0.39 Conformation dependent library (CDL) restraints added in 211.6 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: 0.28 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: 0.46 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: 0.00 - 1.78: 1921 1.78 - 3.56: 323 3.56 - 5.33: 51 5.33 - 7.11: 6 7.11 - 8.89: 9 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 3.120 nonbonded pdb=" OD1 ASP A 7 " pdb=" N GLY A 9 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP D 7 " pdb=" N GLY D 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP E 7 " pdb=" N GLY E 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP C 7 " pdb=" N GLY C 9 " model vdw 2.485 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.730 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.191 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: 0.1346 time to fit residues: 8.4612 Evaluate side-chains 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1728 Z= 0.133 Angle : 0.642 6.233 2310 Z= 0.335 Chirality : 0.052 0.139 234 Planarity : 0.002 0.008 306 Dihedral : 9.553 45.162 257 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.33 % Allowed : 8.93 % Favored : 82.74 % 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: -4.75 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 13 PHE 0.008 0.001 PHE D 19 TYR 0.019 0.004 TYR B 10 ARG 0.002 0.001 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 32 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.164 Fit side-chains REVERT: A 10 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6633 (t80) REVERT: C 3 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7175 (tt0) REVERT: C 5 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7607 (ttm110) REVERT: E 17 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7902 (tt) outliers start: 14 outliers final: 7 residues processed: 31 average time/residue: 0.1252 time to fit residues: 4.6497 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain C residue 10 TYR 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 17 LEU Chi-restraints excluded: chain F residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 1728 Z= 0.208 Angle : 0.696 6.157 2310 Z= 0.375 Chirality : 0.054 0.152 234 Planarity : 0.003 0.012 306 Dihedral : 7.906 56.421 235 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 6.55 % Allowed : 10.12 % Favored : 83.33 % 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: -4.39 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.015 0.002 PHE D 4 TYR 0.028 0.005 TYR B 10 ARG 0.002 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 32 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.194 Fit side-chains REVERT: C 5 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8166 (ttm170) REVERT: C 8 SER cc_start: 0.8724 (m) cc_final: 0.8387 (t) REVERT: D 5 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7471 (mmm-85) REVERT: D 8 SER cc_start: 0.9144 (m) cc_final: 0.8692 (t) outliers start: 11 outliers final: 8 residues processed: 28 average time/residue: 0.1407 time to fit residues: 4.6494 Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 12 VAL 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: 7.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 1728 Z= 0.267 Angle : 0.708 6.246 2310 Z= 0.374 Chirality : 0.055 0.159 234 Planarity : 0.003 0.013 306 Dihedral : 7.680 56.315 233 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.76 % Allowed : 16.67 % Favored : 78.57 % 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: -4.46 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 6 PHE 0.012 0.002 PHE F 20 TYR 0.025 0.005 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 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.195 Fit side-chains REVERT: A 10 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6878 (t80) REVERT: B 5 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8099 (tpp80) REVERT: D 8 SER cc_start: 0.9267 (m) cc_final: 0.8823 (t) outliers start: 8 outliers final: 7 residues processed: 23 average time/residue: 0.1011 time to fit residues: 2.9232 Evaluate side-chains 23 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1728 Z= 0.142 Angle : 0.551 4.953 2310 Z= 0.290 Chirality : 0.048 0.131 234 Planarity : 0.002 0.007 306 Dihedral : 7.133 59.628 233 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.76 % Allowed : 16.07 % Favored : 79.17 % 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 (0.39), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.30), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 13 PHE 0.009 0.002 PHE E 4 TYR 0.017 0.003 TYR B 10 ARG 0.001 0.000 ARG C 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 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.186 Fit side-chains REVERT: A 3 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7522 (tt0) REVERT: B 5 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8174 (tpp80) REVERT: C 8 SER cc_start: 0.8757 (m) cc_final: 0.8460 (t) REVERT: D 8 SER cc_start: 0.9159 (m) cc_final: 0.8894 (t) REVERT: E 10 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7359 (p90) outliers start: 8 outliers final: 7 residues processed: 25 average time/residue: 0.0991 time to fit residues: 3.1163 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL 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 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: 8.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 0.0020 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 6.7996 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 1728 Z= 0.342 Angle : 0.758 8.371 2310 Z= 0.397 Chirality : 0.056 0.155 234 Planarity : 0.004 0.013 306 Dihedral : 8.161 59.279 233 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 4.76 % Allowed : 18.45 % Favored : 76.79 % 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: -4.50 (0.38), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS B 13 PHE 0.014 0.003 PHE A 4 TYR 0.030 0.006 TYR F 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 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.188 Fit side-chains REVERT: A 3 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7473 (tt0) REVERT: A 10 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 5 ARG cc_start: 0.8579 (ttt180) cc_final: 0.8234 (tpp80) REVERT: C 10 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7192 (t80) REVERT: D 8 SER cc_start: 0.9367 (m) cc_final: 0.8912 (t) REVERT: F 1 ASP cc_start: 0.8137 (p0) cc_final: 0.7914 (p0) outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.1258 time to fit residues: 3.9244 Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1728 Z= 0.116 Angle : 0.530 5.492 2310 Z= 0.277 Chirality : 0.048 0.128 234 Planarity : 0.001 0.006 306 Dihedral : 6.968 55.727 233 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.57 % Allowed : 19.64 % Favored : 76.79 % 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: -4.15 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.008 0.002 PHE B 19 TYR 0.015 0.003 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 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.188 Fit side-chains REVERT: A 3 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7466 (tt0) REVERT: B 5 ARG cc_start: 0.8517 (ttt180) cc_final: 0.8275 (tpp80) REVERT: C 8 SER cc_start: 0.8906 (m) cc_final: 0.8648 (t) REVERT: E 10 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7561 (p90) REVERT: F 35 MET cc_start: 0.8336 (mtp) cc_final: 0.8121 (mtt) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0950 time to fit residues: 3.0274 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.0070 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1728 Z= 0.180 Angle : 0.575 5.624 2310 Z= 0.302 Chirality : 0.049 0.133 234 Planarity : 0.002 0.008 306 Dihedral : 7.203 56.068 233 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.17 % Allowed : 19.64 % Favored : 76.19 % 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: -4.15 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.009 0.002 PHE A 4 TYR 0.020 0.004 TYR B 10 ARG 0.001 0.000 ARG F 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 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.194 Fit side-chains REVERT: A 3 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7464 (tt0) REVERT: A 10 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.7095 (t80) REVERT: B 5 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8243 (tpp80) REVERT: E 10 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7488 (p90) REVERT: F 1 ASP cc_start: 0.8196 (p0) cc_final: 0.7938 (p0) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.0967 time to fit residues: 3.2927 Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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: 0.8055 moved from start: 0.7612 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= 0.189 Angle : 0.585 5.532 2310 Z= 0.306 Chirality : 0.049 0.141 234 Planarity : 0.002 0.008 306 Dihedral : 7.291 55.770 233 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.76 % Allowed : 19.05 % Favored : 76.19 % 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: -4.13 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.008 0.002 PHE D 20 TYR 0.020 0.004 TYR B 10 ARG 0.001 0.000 ARG F 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 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.205 Fit side-chains REVERT: A 3 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7489 (tt0) REVERT: A 10 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.7077 (t80) REVERT: B 5 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8208 (tpp80) REVERT: E 10 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7499 (p90) REVERT: F 1 ASP cc_start: 0.8090 (p0) cc_final: 0.7823 (p0) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.0919 time to fit residues: 3.1486 Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.7695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1728 Z= 0.158 Angle : 0.550 5.159 2310 Z= 0.289 Chirality : 0.048 0.128 234 Planarity : 0.002 0.007 306 Dihedral : 7.115 54.995 233 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.76 % Allowed : 19.05 % Favored : 76.19 % 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: -4.05 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 13 PHE 0.007 0.002 PHE D 20 TYR 0.018 0.003 TYR B 10 ARG 0.001 0.000 ARG F 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 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.200 Fit side-chains REVERT: A 3 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7368 (tt0) REVERT: A 10 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.7033 (t80) REVERT: C 8 SER cc_start: 0.9030 (m) cc_final: 0.8678 (t) REVERT: E 10 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7520 (p90) REVERT: F 1 ASP cc_start: 0.8215 (p0) cc_final: 0.7984 (p0) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.1010 time to fit residues: 3.4873 Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 12 VAL 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 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: 5.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4646 r_free = 0.4646 target = 0.142160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.127919 restraints weight = 2632.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.130668 restraints weight = 1158.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.132511 restraints weight = 713.683| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1728 Z= 0.181 Angle : 0.575 5.283 2310 Z= 0.302 Chirality : 0.049 0.132 234 Planarity : 0.002 0.012 306 Dihedral : 7.268 55.108 233 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 5.36 % Allowed : 18.45 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.008 0.002 PHE D 20 TYR 0.019 0.004 TYR B 10 ARG 0.001 0.000 ARG B 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 848.54 seconds wall clock time: 15 minutes 59.12 seconds (959.12 seconds total)