Starting phenix.real_space_refine on Sun Mar 10 21:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j26_35945/03_2024/8j26_35945_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 15 5.16 5 C 3177 2.51 5 N 915 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 90": "OD1" <-> "OD2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" 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: 5406 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 994 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1548 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1111 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.67 Number of scatterers: 5406 At special positions: 0 Unit cell: (67.158, 109.746, 109.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 90 15.00 O 1209 8.00 N 915 7.00 C 3177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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 Links applied NAG-ASN " NAG C 701 " - " ASN C 343 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 671.5 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 7 sheets defined 10.5% alpha, 24.8% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.832A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.200A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 11 removed outlier: 5.602A pdb=" N LYS A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 17 through 23 Processing sheet with id= C, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.506A pdb=" N SER A 36 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= E, first strand: chain 'B' and resid 114 through 116 removed outlier: 5.881A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.698A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 452 through 454 78 hydrogen bonds defined for protein. 195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 665 1.30 - 1.43: 2233 1.43 - 1.57: 2599 1.57 - 1.70: 229 1.70 - 1.84: 26 Bond restraints: 5752 Sorted by residual: bond pdb=" C2' 85Y D 24 " pdb=" C1' 85Y D 24 " ideal model delta sigma weight residual 1.280 1.571 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C2' 85Y D 43 " pdb=" C1' 85Y D 43 " ideal model delta sigma weight residual 1.280 1.571 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C2' 85Y E 55 " pdb=" C1' 85Y E 55 " ideal model delta sigma weight residual 1.280 1.567 -0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2' 85Y D 34 " pdb=" C1' 85Y D 34 " ideal model delta sigma weight residual 1.280 1.566 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C2' 85Y E 59 " pdb=" C1' 85Y E 59 " ideal model delta sigma weight residual 1.280 1.565 -0.285 2.00e-02 2.50e+03 2.04e+02 ... (remaining 5747 not shown) Histogram of bond angle deviations from ideal: 90.27 - 102.24: 55 102.24 - 114.22: 3666 114.22 - 126.19: 4169 126.19 - 138.16: 306 138.16 - 150.13: 19 Bond angle restraints: 8215 Sorted by residual: angle pdb=" C23 85Y D 34 " pdb=" C24 85Y D 34 " pdb=" C25 85Y D 34 " ideal model delta sigma weight residual 125.08 150.13 -25.05 3.00e+00 1.11e-01 6.97e+01 angle pdb=" C23 85Y D 30 " pdb=" C24 85Y D 30 " pdb=" C25 85Y D 30 " ideal model delta sigma weight residual 125.08 149.62 -24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" C23 85Y E 48 " pdb=" C24 85Y E 48 " pdb=" C25 85Y E 48 " ideal model delta sigma weight residual 125.08 148.87 -23.79 3.00e+00 1.11e-01 6.29e+01 angle pdb=" C23 85Y D 43 " pdb=" C24 85Y D 43 " pdb=" C25 85Y D 43 " ideal model delta sigma weight residual 125.08 148.78 -23.70 3.00e+00 1.11e-01 6.24e+01 angle pdb=" C23 85Y D 41 " pdb=" C24 85Y D 41 " pdb=" C25 85Y D 41 " ideal model delta sigma weight residual 125.08 148.75 -23.67 3.00e+00 1.11e-01 6.23e+01 ... (remaining 8210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 2583 35.70 - 71.41: 388 71.41 - 107.11: 19 107.11 - 142.82: 4 142.82 - 178.52: 10 Dihedral angle restraints: 3004 sinusoidal: 1778 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 17.27 75.73 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.67 50.33 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" C20 85Y E 34 " pdb=" C23 85Y E 34 " pdb=" N22 85Y E 34 " pdb=" C24 85Y E 34 " ideal model delta sinusoidal sigma weight residual 123.57 -52.47 176.04 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 601 0.046 - 0.092: 171 0.092 - 0.138: 45 0.138 - 0.184: 18 0.184 - 0.230: 3 Chirality restraints: 838 Sorted by residual: chirality pdb=" C3' 85Y E 59 " pdb=" C4' 85Y E 59 " pdb=" O3' 85Y E 59 " pdb=" C2' 85Y E 59 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' 85Y D 17 " pdb=" C4' 85Y D 17 " pdb=" O3' 85Y D 17 " pdb=" C2' 85Y D 17 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1' 85Y D 43 " pdb=" O4' 85Y D 43 " pdb=" C2' 85Y D 43 " pdb=" N1 85Y D 43 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 835 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 37 " 0.009 2.00e-02 2.50e+03 8.43e-03 1.78e+00 pdb=" CG TRP A 37 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 37 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 37 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 85Y D 17 " 0.001 2.00e-02 2.50e+03 6.31e-03 9.96e-01 pdb=" N1 85Y D 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 85Y D 17 " 0.001 2.00e-02 2.50e+03 pdb=" O2 85Y D 17 " 0.002 2.00e-02 2.50e+03 pdb=" N3 85Y D 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 85Y D 17 " 0.001 2.00e-02 2.50e+03 pdb=" O4 85Y D 17 " -0.000 2.00e-02 2.50e+03 pdb=" C5 85Y D 17 " -0.017 2.00e-02 2.50e+03 pdb=" C6 85Y D 17 " 0.003 2.00e-02 2.50e+03 pdb=" C20 85Y D 17 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 89 " -0.005 2.00e-02 2.50e+03 9.69e-03 9.39e-01 pdb=" C GLU B 89 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU B 89 " -0.006 2.00e-02 2.50e+03 pdb=" N ASP B 90 " -0.006 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 163 2.63 - 3.20: 4873 3.20 - 3.77: 8614 3.77 - 4.33: 11634 4.33 - 4.90: 18216 Nonbonded interactions: 43500 Sorted by model distance: nonbonded pdb=" OH TYR B 35 " pdb=" O ASP B 104 " model vdw 2.066 2.440 nonbonded pdb=" N6 DA E 35 " pdb=" O SER C 494 " model vdw 2.067 2.520 nonbonded pdb=" O2 DC E 36 " pdb=" OH TYR C 505 " model vdw 2.074 2.440 nonbonded pdb=" OP2 85Y D 43 " pdb=" O3' 85Y D 43 " model vdw 2.123 2.440 nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 360 " model vdw 2.138 2.440 ... (remaining 43495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 11.150 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 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 : 0.028 0.291 5752 Z= 1.384 Angle : 1.812 25.054 8215 Z= 0.651 Chirality : 0.051 0.230 838 Planarity : 0.002 0.012 721 Dihedral : 28.183 178.520 2216 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.56 % Allowed : 23.46 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.41), residues: 421 helix: -3.59 (0.67), residues: 32 sheet: -0.36 (0.47), residues: 128 loop : -0.36 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 37 HIS 0.001 0.000 HIS C 519 PHE 0.012 0.001 PHE B 29 TYR 0.016 0.001 TYR B 35 ARG 0.001 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.443 Fit side-chains REVERT: A 72 THR cc_start: 0.8726 (m) cc_final: 0.8342 (p) REVERT: C 383 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7908 (p) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1930 time to fit residues: 11.5488 Evaluate side-chains 40 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5752 Z= 0.207 Angle : 1.253 13.827 8215 Z= 0.480 Chirality : 0.041 0.214 838 Planarity : 0.003 0.012 721 Dihedral : 30.913 179.276 1511 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.19 % Allowed : 24.58 % Favored : 71.23 % 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: -0.87 (0.41), residues: 421 helix: -3.13 (0.82), residues: 32 sheet: -0.18 (0.46), residues: 128 loop : -0.37 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 37 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE C 392 TYR 0.012 0.001 TYR B 102 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7802 (p0) cc_final: 0.7067 (m-30) REVERT: A 72 THR cc_start: 0.8733 (m) cc_final: 0.8343 (p) REVERT: A 98 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8465 (p) outliers start: 15 outliers final: 7 residues processed: 52 average time/residue: 0.1782 time to fit residues: 12.2377 Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.6615 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5752 Z= 0.279 Angle : 1.274 13.842 8215 Z= 0.491 Chirality : 0.042 0.236 838 Planarity : 0.003 0.017 721 Dihedral : 31.015 179.525 1510 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.91 % Allowed : 25.98 % Favored : 70.11 % 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: -0.92 (0.41), residues: 421 helix: -3.16 (0.81), residues: 32 sheet: -0.15 (0.46), residues: 129 loop : -0.45 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 37 HIS 0.002 0.001 HIS A 41 PHE 0.009 0.001 PHE C 392 TYR 0.016 0.001 TYR B 102 ARG 0.002 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.368 Fit side-chains REVERT: A 72 THR cc_start: 0.8777 (m) cc_final: 0.8399 (p) REVERT: A 98 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8573 (p) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1810 time to fit residues: 12.3706 Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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: 0.6554 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5752 Z= 0.206 Angle : 1.236 13.747 8215 Z= 0.473 Chirality : 0.040 0.230 838 Planarity : 0.002 0.016 721 Dihedral : 30.885 179.879 1509 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.91 % Allowed : 24.86 % Favored : 71.23 % 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: -1.04 (0.41), residues: 421 helix: -3.02 (0.83), residues: 32 sheet: -0.38 (0.45), residues: 135 loop : -0.47 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 37 HIS 0.001 0.001 HIS A 41 PHE 0.008 0.001 PHE C 392 TYR 0.013 0.001 TYR B 35 ARG 0.001 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.438 Fit side-chains REVERT: A 72 THR cc_start: 0.8753 (m) cc_final: 0.8374 (p) REVERT: A 98 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8520 (p) outliers start: 14 outliers final: 10 residues processed: 51 average time/residue: 0.1892 time to fit residues: 12.9654 Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5752 Z= 0.318 Angle : 1.298 14.131 8215 Z= 0.505 Chirality : 0.043 0.239 838 Planarity : 0.003 0.020 721 Dihedral : 31.209 178.906 1509 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.47 % Allowed : 24.30 % Favored : 71.23 % 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: -0.94 (0.41), residues: 421 helix: -3.32 (0.81), residues: 26 sheet: -0.16 (0.46), residues: 127 loop : -0.52 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 37 HIS 0.002 0.001 HIS A 41 PHE 0.007 0.001 PHE C 456 TYR 0.017 0.002 TYR B 35 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.452 Fit side-chains REVERT: A 72 THR cc_start: 0.8820 (m) cc_final: 0.8445 (p) REVERT: A 98 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8732 (p) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1777 time to fit residues: 11.9817 Evaluate side-chains 49 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.6591 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5752 Z= 0.206 Angle : 1.243 13.801 8215 Z= 0.477 Chirality : 0.040 0.228 838 Planarity : 0.002 0.019 721 Dihedral : 30.956 177.989 1509 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.91 % Allowed : 24.86 % Favored : 71.23 % 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: -1.09 (0.41), residues: 421 helix: -3.11 (0.87), residues: 26 sheet: -0.55 (0.45), residues: 134 loop : -0.49 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 99 HIS 0.002 0.001 HIS A 41 PHE 0.007 0.001 PHE A 64 TYR 0.013 0.001 TYR B 35 ARG 0.001 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.482 Fit side-chains REVERT: A 98 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 383 SER cc_start: 0.8080 (t) cc_final: 0.7775 (p) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.1775 time to fit residues: 11.7449 Evaluate side-chains 50 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6617 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5752 Z= 0.222 Angle : 1.245 13.608 8215 Z= 0.478 Chirality : 0.040 0.228 838 Planarity : 0.002 0.018 721 Dihedral : 30.951 178.771 1509 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.35 % Allowed : 25.14 % Favored : 71.51 % 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: -0.99 (0.41), residues: 421 helix: -3.00 (0.88), residues: 26 sheet: -0.19 (0.46), residues: 127 loop : -0.61 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 37 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE C 392 TYR 0.013 0.001 TYR B 35 ARG 0.002 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.545 Fit side-chains REVERT: A 98 THR cc_start: 0.8906 (m) cc_final: 0.8667 (p) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.1808 time to fit residues: 11.9792 Evaluate side-chains 49 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.6577 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5752 Z= 0.197 Angle : 1.231 13.409 8215 Z= 0.472 Chirality : 0.040 0.228 838 Planarity : 0.002 0.018 721 Dihedral : 30.866 178.351 1509 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.07 % Allowed : 25.98 % Favored : 70.95 % 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: -1.27 (0.41), residues: 421 helix: -2.74 (0.86), residues: 32 sheet: -0.63 (0.45), residues: 136 loop : -0.63 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 99 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE C 392 TYR 0.012 0.001 TYR B 35 ARG 0.001 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.464 Fit side-chains REVERT: A 98 THR cc_start: 0.8834 (m) cc_final: 0.8594 (p) outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.1831 time to fit residues: 12.3160 Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5752 Z= 0.192 Angle : 1.228 13.222 8215 Z= 0.471 Chirality : 0.040 0.226 838 Planarity : 0.002 0.018 721 Dihedral : 30.799 178.436 1509 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.35 % Allowed : 25.98 % Favored : 70.67 % 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: -1.26 (0.40), residues: 421 helix: -2.54 (0.89), residues: 32 sheet: -0.61 (0.45), residues: 135 loop : -0.67 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE C 392 TYR 0.011 0.001 TYR B 35 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.480 Fit side-chains REVERT: A 25 THR cc_start: 0.8407 (p) cc_final: 0.7932 (t) REVERT: A 28 ASP cc_start: 0.7560 (p0) cc_final: 0.6908 (p0) REVERT: A 98 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8615 (p) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.1802 time to fit residues: 11.8257 Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.6545 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5752 Z= 0.187 Angle : 1.225 13.063 8215 Z= 0.470 Chirality : 0.039 0.224 838 Planarity : 0.002 0.019 721 Dihedral : 30.747 178.434 1509 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.51 % Allowed : 26.54 % Favored : 70.95 % 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: -1.25 (0.40), residues: 421 helix: -2.36 (0.93), residues: 32 sheet: -0.67 (0.45), residues: 136 loop : -0.64 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 99 HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE C 392 TYR 0.011 0.001 TYR B 35 ARG 0.002 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.448 Fit side-chains REVERT: A 72 THR cc_start: 0.8694 (m) cc_final: 0.8279 (p) REVERT: A 98 THR cc_start: 0.8761 (m) cc_final: 0.8534 (p) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.1815 time to fit residues: 11.1816 Evaluate side-chains 46 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.104970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080261 restraints weight = 14781.108| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.50 r_work: 0.3255 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5752 Z= 0.238 Angle : 1.250 13.486 8215 Z= 0.482 Chirality : 0.041 0.228 838 Planarity : 0.003 0.018 721 Dihedral : 30.946 178.800 1509 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.79 % Allowed : 26.82 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.40), residues: 421 helix: -2.45 (0.91), residues: 32 sheet: -0.37 (0.47), residues: 128 loop : -0.71 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A 41 PHE 0.006 0.001 PHE C 392 TYR 0.014 0.001 TYR B 35 ARG 0.002 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.18 seconds wall clock time: 28 minutes 37.15 seconds (1717.15 seconds total)