Starting phenix.real_space_refine on Fri Nov 15 05:02:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jew_36201/11_2024/8jew_36201.cif" } resolution = 2.49 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 Na 4 4.78 5 C 5504 2.51 5 N 1246 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3881 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 478} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Unusual residues: {' NA': 2, 'ASC': 1, 'AV0': 2, 'CLR': 2, 'LBN': 1, 'NAG': 1, 'PLM': 1} Classifications: {'undetermined': 10, 'water': 3} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PLM:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.76, per 1000 atoms: 0.94 Number of scatterers: 8284 At special positions: 0 Unit cell: (94.62, 108.564, 77.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 2 15.00 Na 4 11.00 O 1470 8.00 N 1246 7.00 C 5504 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 74.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 removed outlier: 3.720A pdb=" N LEU A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.775A pdb=" N PHE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 101 Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.860A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.559A pdb=" N ILE A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 Proline residue: A 151 - end of helix removed outlier: 3.562A pdb=" N GLU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.894A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 274 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.895A pdb=" N SER A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.682A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.715A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.540A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 454 through 478 Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 479 through 482 removed outlier: 4.509A pdb=" N ILE A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.720A pdb=" N LEU B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.775A pdb=" N PHE B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 101 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.860A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.559A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 173 Proline residue: B 151 - end of helix removed outlier: 3.562A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.894A pdb=" N LEU B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 255 through 274 Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 317 through 346 removed outlier: 3.895A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 374 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.682A pdb=" N ILE B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.715A pdb=" N VAL B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.540A pdb=" N THR B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 454 through 478 Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 479 through 482 removed outlier: 4.509A pdb=" N ILE B 482 " --> pdb=" O PRO B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 556 through 561 Processing sheet with id=1, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=2, first strand: chain 'B' and resid 108 through 110 506 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1206 1.31 - 1.44: 2212 1.44 - 1.58: 4978 1.58 - 1.71: 4 1.71 - 1.84: 88 Bond restraints: 8488 Sorted by residual: bond pdb=" C TYR B 474 " pdb=" O TYR B 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C TYR A 474 " pdb=" O TYR A 474 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" C PRO A 301 " pdb=" O PRO A 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C PRO B 301 " pdb=" O PRO B 301 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.06e+01 bond pdb=" C GLN B 287 " pdb=" O GLN B 287 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.35e-02 5.49e+03 1.98e+01 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8676 2.07 - 4.14: 2672 4.14 - 6.21: 224 6.21 - 8.29: 12 8.29 - 10.36: 4 Bond angle restraints: 11588 Sorted by residual: angle pdb=" N TYR A 42 " pdb=" CA TYR A 42 " pdb=" C TYR A 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" N TYR B 42 " pdb=" CA TYR B 42 " pdb=" C TYR B 42 " ideal model delta sigma weight residual 111.71 106.27 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" CA ILE A 218 " pdb=" C ILE A 218 " pdb=" O ILE A 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" CA ILE B 218 " pdb=" C ILE B 218 " pdb=" O ILE B 218 " ideal model delta sigma weight residual 121.17 116.22 4.95 1.06e+00 8.90e-01 2.18e+01 angle pdb=" O ILE A 218 " pdb=" C ILE A 218 " pdb=" N LEU A 219 " ideal model delta sigma weight residual 121.91 126.38 -4.47 9.80e-01 1.04e+00 2.08e+01 ... (remaining 11583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 5262 28.32 - 56.64: 200 56.64 - 84.95: 32 84.95 - 113.27: 0 113.27 - 141.59: 8 Dihedral angle restraints: 5502 sinusoidal: 2602 harmonic: 2900 Sorted by residual: dihedral pdb=" C1 LBN B 605 " pdb=" O1 LBN B 605 " pdb=" P1 LBN B 605 " pdb=" O3 LBN B 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C1 LBN A 605 " pdb=" O1 LBN A 605 " pdb=" P1 LBN A 605 " pdb=" O3 LBN A 605 " ideal model delta sinusoidal sigma weight residual -84.60 56.99 -141.59 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O5 LBN A 605 " pdb=" C2 LBN A 605 " pdb=" C3 LBN A 605 " pdb=" O7 LBN A 605 " ideal model delta sinusoidal sigma weight residual 62.67 -60.77 123.44 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 630 0.049 - 0.098: 436 0.098 - 0.147: 232 0.147 - 0.196: 100 0.196 - 0.244: 24 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA PRO B 563 " pdb=" N PRO B 563 " pdb=" C PRO B 563 " pdb=" CB PRO B 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 563 " pdb=" N PRO A 563 " pdb=" C PRO A 563 " pdb=" CB PRO A 563 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TRP B 149 " pdb=" N TRP B 149 " pdb=" C TRP B 149 " pdb=" CB TRP B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1419 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG A 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 609 " -0.056 2.00e-02 2.50e+03 4.63e-02 2.67e+01 pdb=" C7 NAG B 609 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B 609 " -0.040 2.00e-02 2.50e+03 pdb=" N2 NAG B 609 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 609 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.027 2.00e-02 2.50e+03 2.91e-02 2.11e+01 pdb=" CG TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " -0.019 2.00e-02 2.50e+03 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 32 2.53 - 3.12: 6304 3.12 - 3.71: 13560 3.71 - 4.31: 19920 4.31 - 4.90: 32382 Nonbonded interactions: 72198 Sorted by model distance: nonbonded pdb=" OD2 ASP A 338 " pdb="NA NA A 602 " model vdw 1.932 2.470 nonbonded pdb=" OD2 ASP B 338 " pdb="NA NA B 602 " model vdw 1.932 2.470 nonbonded pdb=" ND2 ASN B 144 " pdb=" C1 NAG B 609 " model vdw 2.059 3.550 nonbonded pdb=" ND2 ASN A 144 " pdb=" C1 NAG A 609 " model vdw 2.059 3.550 nonbonded pdb=" OAI AV0 A 604 " pdb=" OH TYR B 474 " model vdw 2.228 3.040 ... (remaining 72193 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.015 0.069 8488 Z= 0.973 Angle : 1.791 10.357 11588 Z= 1.295 Chirality : 0.085 0.244 1422 Planarity : 0.014 0.117 1352 Dihedral : 15.566 141.589 3650 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.48 % Allowed : 12.38 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.48 (0.24), residues: 1012 helix: -0.06 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.012 TRP A 311 HIS 0.014 0.005 HIS A 210 PHE 0.050 0.010 PHE A 459 TYR 0.043 0.009 TYR B 474 ARG 0.021 0.003 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.927 Fit side-chains REVERT: A 78 MET cc_start: 0.8861 (tmt) cc_final: 0.8390 (tmt) REVERT: A 99 THR cc_start: 0.8314 (t) cc_final: 0.8100 (p) REVERT: A 119 LYS cc_start: 0.7518 (pttp) cc_final: 0.7301 (mtmm) REVERT: A 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8324 (mtm) REVERT: A 172 LEU cc_start: 0.8139 (tp) cc_final: 0.7673 (mt) REVERT: A 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7092 (mt0) REVERT: A 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6770 (pt) REVERT: A 334 GLU cc_start: 0.8383 (tt0) cc_final: 0.8141 (tt0) REVERT: A 381 SER cc_start: 0.8036 (m) cc_final: 0.7664 (p) REVERT: A 476 GLU cc_start: 0.7849 (tp30) cc_final: 0.7310 (mm-30) REVERT: A 500 GLU cc_start: 0.7758 (mp0) cc_final: 0.7470 (mp0) REVERT: A 550 MET cc_start: 0.3350 (tpt) cc_final: 0.3060 (tpt) REVERT: B 78 MET cc_start: 0.8858 (tmt) cc_final: 0.8387 (tmt) REVERT: B 99 THR cc_start: 0.8316 (t) cc_final: 0.8101 (p) REVERT: B 119 LYS cc_start: 0.7520 (pttp) cc_final: 0.7302 (mtmm) REVERT: B 161 MET cc_start: 0.8740 (mtp) cc_final: 0.8323 (mtm) REVERT: B 172 LEU cc_start: 0.8133 (tp) cc_final: 0.7668 (mt) REVERT: B 201 GLN cc_start: 0.8477 (tp40) cc_final: 0.7093 (mt0) REVERT: B 251 ILE cc_start: 0.7110 (tt) cc_final: 0.6772 (pt) REVERT: B 334 GLU cc_start: 0.8380 (tt0) cc_final: 0.8139 (tt0) REVERT: B 381 SER cc_start: 0.8037 (m) cc_final: 0.7664 (p) REVERT: B 476 GLU cc_start: 0.7850 (tp30) cc_final: 0.7312 (mm-30) REVERT: B 500 GLU cc_start: 0.7762 (mp0) cc_final: 0.7473 (mp0) REVERT: B 550 MET cc_start: 0.3351 (tpt) cc_final: 0.3063 (tpt) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 1.1823 time to fit residues: 187.1956 Evaluate side-chains 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 147 HIS B 483 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 8488 Z= 0.387 Angle : 1.243 39.130 11588 Z= 0.572 Chirality : 0.066 0.513 1422 Planarity : 0.013 0.192 1352 Dihedral : 12.970 127.441 1940 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.99 % Allowed : 2.27 % Favored : 96.74 % Rotamer: Outliers : 4.29 % Allowed : 13.69 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.37 (0.26), residues: 1012 helix: 0.19 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP B 265 HIS 0.058 0.007 HIS B 210 PHE 0.100 0.006 PHE B 255 TYR 0.181 0.008 TYR B 402 ARG 0.067 0.005 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.943 Fit side-chains REVERT: A 78 MET cc_start: 0.8682 (tmt) cc_final: 0.8176 (tmt) REVERT: A 161 MET cc_start: 0.8564 (mtp) cc_final: 0.8107 (mtm) REVERT: A 172 LEU cc_start: 0.8047 (tp) cc_final: 0.7582 (mt) REVERT: A 251 ILE cc_start: 0.7067 (tt) cc_final: 0.6756 (pt) REVERT: A 381 SER cc_start: 0.7816 (m) cc_final: 0.7505 (p) REVERT: A 476 GLU cc_start: 0.7866 (tp30) cc_final: 0.7361 (pt0) REVERT: A 500 GLU cc_start: 0.7731 (mp0) cc_final: 0.7379 (mp0) REVERT: A 550 MET cc_start: 0.3433 (tpt) cc_final: 0.3143 (tpt) REVERT: B 78 MET cc_start: 0.8628 (tmt) cc_final: 0.8109 (tmt) REVERT: B 119 LYS cc_start: 0.7213 (pttp) cc_final: 0.6928 (mtmm) REVERT: B 133 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6530 (tp30) REVERT: B 172 LEU cc_start: 0.7903 (tp) cc_final: 0.7447 (OUTLIER) REVERT: B 249 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4297 (mm) REVERT: B 251 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6897 (pt) REVERT: B 282 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7184 (mtpm) REVERT: B 476 GLU cc_start: 0.7653 (tp30) cc_final: 0.7094 (mp0) REVERT: B 500 GLU cc_start: 0.7638 (mp0) cc_final: 0.7421 (mp0) REVERT: B 550 MET cc_start: 0.3537 (tpt) cc_final: 0.3253 (tpt) outliers start: 36 outliers final: 8 residues processed: 159 average time/residue: 1.0630 time to fit residues: 181.3449 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.0010 overall best weight: 1.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 108 GLN B 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8488 Z= 0.184 Angle : 0.633 8.431 11588 Z= 0.306 Chirality : 0.042 0.172 1422 Planarity : 0.005 0.046 1352 Dihedral : 12.430 131.485 1940 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.67 % Allowed : 15.95 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.24 (0.26), residues: 1012 helix: 1.23 (0.19), residues: 676 sheet: None (None), residues: 0 loop : 0.15 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.003 0.001 HIS B 354 PHE 0.017 0.002 PHE B 502 TYR 0.014 0.001 TYR B 339 ARG 0.006 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.953 Fit side-chains REVERT: A 161 MET cc_start: 0.8542 (mtp) cc_final: 0.8082 (mtm) REVERT: A 172 LEU cc_start: 0.7917 (tp) cc_final: 0.7528 (mt) REVERT: A 251 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6698 (pt) REVERT: A 381 SER cc_start: 0.7907 (m) cc_final: 0.7557 (p) REVERT: A 476 GLU cc_start: 0.7803 (tp30) cc_final: 0.7324 (pt0) REVERT: A 550 MET cc_start: 0.3614 (tpt) cc_final: 0.3290 (tpt) REVERT: B 119 LYS cc_start: 0.7289 (pttp) cc_final: 0.7029 (mtmm) REVERT: B 172 LEU cc_start: 0.7856 (tp) cc_final: 0.7324 (mt) REVERT: B 251 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6979 (pt) REVERT: B 282 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7216 (mtpm) REVERT: B 381 SER cc_start: 0.7836 (m) cc_final: 0.7456 (p) REVERT: B 476 GLU cc_start: 0.7934 (tp30) cc_final: 0.7416 (mp0) REVERT: B 550 MET cc_start: 0.3614 (tpt) cc_final: 0.3296 (tpt) outliers start: 14 outliers final: 4 residues processed: 128 average time/residue: 1.0485 time to fit residues: 144.5708 Evaluate side-chains 123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 0.0060 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8488 Z= 0.181 Angle : 0.598 7.532 11588 Z= 0.289 Chirality : 0.041 0.133 1422 Planarity : 0.005 0.050 1352 Dihedral : 12.187 134.585 1940 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.50 % Allowed : 15.12 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.96 (0.26), residues: 1012 helix: 1.63 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 0.82 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.002 0.001 HIS B 354 PHE 0.016 0.002 PHE B 361 TYR 0.008 0.001 TYR B 339 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.855 Fit side-chains REVERT: A 78 MET cc_start: 0.8622 (tmt) cc_final: 0.8223 (tmt) REVERT: A 161 MET cc_start: 0.8529 (mtp) cc_final: 0.8085 (mtm) REVERT: A 172 LEU cc_start: 0.7896 (tp) cc_final: 0.7510 (mt) REVERT: A 251 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6688 (pt) REVERT: A 381 SER cc_start: 0.7857 (m) cc_final: 0.7433 (p) REVERT: A 476 GLU cc_start: 0.7856 (tp30) cc_final: 0.7254 (mp0) REVERT: A 550 MET cc_start: 0.3620 (tpt) cc_final: 0.3323 (tpt) REVERT: B 116 VAL cc_start: 0.7913 (t) cc_final: 0.7672 (t) REVERT: B 119 LYS cc_start: 0.7289 (pttp) cc_final: 0.6972 (mtmm) REVERT: B 172 LEU cc_start: 0.7951 (tp) cc_final: 0.7433 (mt) REVERT: B 251 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6867 (pt) REVERT: B 282 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7174 (mtpm) REVERT: B 381 SER cc_start: 0.7824 (m) cc_final: 0.7459 (p) REVERT: B 476 GLU cc_start: 0.7887 (tp30) cc_final: 0.7260 (mp0) REVERT: B 550 MET cc_start: 0.3623 (tpt) cc_final: 0.3205 (tpt) outliers start: 21 outliers final: 8 residues processed: 127 average time/residue: 1.0931 time to fit residues: 149.0572 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8488 Z= 0.352 Angle : 0.732 8.296 11588 Z= 0.356 Chirality : 0.047 0.173 1422 Planarity : 0.006 0.051 1352 Dihedral : 12.876 133.586 1940 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.86 % Allowed : 15.71 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.67 (0.26), residues: 1012 helix: 1.37 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.84 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 149 HIS 0.004 0.001 HIS B 51 PHE 0.024 0.003 PHE A 200 TYR 0.015 0.002 TYR A 42 ARG 0.009 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.936 Fit side-chains REVERT: A 161 MET cc_start: 0.8551 (mtp) cc_final: 0.8163 (mtm) REVERT: A 172 LEU cc_start: 0.7996 (tp) cc_final: 0.7556 (mt) REVERT: A 251 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6646 (pt) REVERT: A 476 GLU cc_start: 0.7878 (tp30) cc_final: 0.7367 (pt0) REVERT: A 550 MET cc_start: 0.3635 (tpt) cc_final: 0.3213 (tpt) REVERT: B 119 LYS cc_start: 0.7367 (pttp) cc_final: 0.7106 (mtmm) REVERT: B 172 LEU cc_start: 0.8039 (tp) cc_final: 0.7575 (mt) REVERT: B 251 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6902 (pt) REVERT: B 282 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7129 (mtpm) REVERT: B 381 SER cc_start: 0.7938 (m) cc_final: 0.7489 (p) REVERT: B 476 GLU cc_start: 0.7931 (tp30) cc_final: 0.7393 (pt0) REVERT: B 500 GLU cc_start: 0.7749 (mp0) cc_final: 0.7497 (mp0) REVERT: B 550 MET cc_start: 0.3570 (tpt) cc_final: 0.3172 (tpt) outliers start: 24 outliers final: 11 residues processed: 130 average time/residue: 1.1315 time to fit residues: 157.6883 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8488 Z= 0.269 Angle : 0.672 8.735 11588 Z= 0.324 Chirality : 0.044 0.156 1422 Planarity : 0.006 0.049 1352 Dihedral : 12.739 133.654 1940 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.86 (0.26), residues: 1012 helix: 1.49 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.97 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 149 HIS 0.003 0.001 HIS B 51 PHE 0.019 0.002 PHE A 436 TYR 0.013 0.002 TYR A 42 ARG 0.006 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.720 Fit side-chains REVERT: A 161 MET cc_start: 0.8531 (mtp) cc_final: 0.8078 (mtm) REVERT: A 172 LEU cc_start: 0.7978 (tp) cc_final: 0.7550 (mt) REVERT: A 251 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6669 (pt) REVERT: A 476 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: A 550 MET cc_start: 0.3699 (tpt) cc_final: 0.3179 (tpt) REVERT: B 119 LYS cc_start: 0.7432 (pttp) cc_final: 0.7137 (mtmm) REVERT: B 172 LEU cc_start: 0.7983 (tp) cc_final: 0.7570 (mt) REVERT: B 251 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6990 (pt) REVERT: B 282 LYS cc_start: 0.7618 (mtmm) cc_final: 0.7174 (mtpm) REVERT: B 381 SER cc_start: 0.7916 (m) cc_final: 0.7528 (p) REVERT: B 476 GLU cc_start: 0.8057 (tp30) cc_final: 0.7526 (pt0) REVERT: B 500 GLU cc_start: 0.7738 (mp0) cc_final: 0.7485 (mp0) outliers start: 26 outliers final: 12 residues processed: 121 average time/residue: 1.3313 time to fit residues: 172.0203 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 412 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 74 HIS ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8488 Z= 0.194 Angle : 0.613 8.179 11588 Z= 0.295 Chirality : 0.042 0.138 1422 Planarity : 0.005 0.048 1352 Dihedral : 12.320 134.300 1940 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.62 % Allowed : 16.67 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.27), residues: 1012 helix: 1.66 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.18 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 149 HIS 0.002 0.001 HIS B 354 PHE 0.015 0.002 PHE A 459 TYR 0.009 0.001 TYR A 42 ARG 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.948 Fit side-chains REVERT: A 161 MET cc_start: 0.8543 (mtp) cc_final: 0.8102 (mtm) REVERT: A 172 LEU cc_start: 0.7939 (tp) cc_final: 0.7520 (mt) REVERT: A 251 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6685 (pt) REVERT: A 381 SER cc_start: 0.7872 (m) cc_final: 0.7453 (p) REVERT: A 452 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: A 476 GLU cc_start: 0.7855 (tp30) cc_final: 0.7240 (mp0) REVERT: A 550 MET cc_start: 0.3702 (tpt) cc_final: 0.3155 (tpt) REVERT: B 116 VAL cc_start: 0.7880 (t) cc_final: 0.7644 (t) REVERT: B 119 LYS cc_start: 0.7302 (pttp) cc_final: 0.6995 (mtmm) REVERT: B 172 LEU cc_start: 0.7938 (tp) cc_final: 0.7496 (mt) REVERT: B 251 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6943 (pt) REVERT: B 282 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7279 (mtpm) REVERT: B 381 SER cc_start: 0.7904 (m) cc_final: 0.7531 (p) REVERT: B 476 GLU cc_start: 0.7979 (tp30) cc_final: 0.7446 (pt0) outliers start: 22 outliers final: 10 residues processed: 122 average time/residue: 1.1352 time to fit residues: 148.2669 Evaluate side-chains 124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 74 HIS A 76 GLN A 483 ASN B 50 GLN B 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8488 Z= 0.167 Angle : 0.586 8.034 11588 Z= 0.281 Chirality : 0.041 0.136 1422 Planarity : 0.005 0.046 1352 Dihedral : 11.967 136.110 1940 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 17.14 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.27), residues: 1012 helix: 1.87 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.35 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.000 HIS A 354 PHE 0.016 0.002 PHE B 361 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.956 Fit side-chains REVERT: A 161 MET cc_start: 0.8520 (mtp) cc_final: 0.8089 (mtm) REVERT: A 172 LEU cc_start: 0.7879 (tp) cc_final: 0.7451 (mt) REVERT: A 251 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6662 (pt) REVERT: A 381 SER cc_start: 0.7841 (m) cc_final: 0.7431 (p) REVERT: A 452 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: A 476 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 550 MET cc_start: 0.3625 (tpt) cc_final: 0.3016 (tpt) REVERT: B 119 LYS cc_start: 0.7353 (pttp) cc_final: 0.7041 (mtmm) REVERT: B 172 LEU cc_start: 0.7859 (tp) cc_final: 0.7459 (mt) REVERT: B 251 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6973 (pt) REVERT: B 381 SER cc_start: 0.7815 (m) cc_final: 0.7458 (p) REVERT: B 452 MET cc_start: 0.8287 (mmp) cc_final: 0.8083 (mmm) REVERT: B 476 GLU cc_start: 0.7967 (tp30) cc_final: 0.7294 (mp0) REVERT: B 500 GLU cc_start: 0.7509 (mp0) cc_final: 0.7178 (mp0) outliers start: 19 outliers final: 11 residues processed: 124 average time/residue: 1.1776 time to fit residues: 156.0482 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 407 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8488 Z= 0.228 Angle : 0.633 7.753 11588 Z= 0.306 Chirality : 0.043 0.142 1422 Planarity : 0.005 0.045 1352 Dihedral : 12.180 135.400 1940 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.02 % Allowed : 17.26 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1012 helix: 1.70 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.29 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.018 0.002 PHE A 420 TYR 0.011 0.001 TYR A 42 ARG 0.005 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.954 Fit side-chains REVERT: A 161 MET cc_start: 0.8520 (mtp) cc_final: 0.8074 (mtm) REVERT: A 172 LEU cc_start: 0.7951 (tp) cc_final: 0.7528 (mt) REVERT: A 251 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6676 (pt) REVERT: A 452 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: A 476 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: A 550 MET cc_start: 0.3616 (tpt) cc_final: 0.3003 (tpt) REVERT: B 119 LYS cc_start: 0.7398 (pttp) cc_final: 0.7115 (mtmm) REVERT: B 172 LEU cc_start: 0.7914 (tp) cc_final: 0.7467 (mt) REVERT: B 251 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6999 (pt) REVERT: B 381 SER cc_start: 0.7868 (m) cc_final: 0.7466 (p) REVERT: B 476 GLU cc_start: 0.7954 (tp30) cc_final: 0.7317 (mp0) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 1.2310 time to fit residues: 147.4178 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 11 optimal weight: 0.3980 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8488 Z= 0.182 Angle : 0.598 7.819 11588 Z= 0.288 Chirality : 0.041 0.135 1422 Planarity : 0.005 0.045 1352 Dihedral : 11.993 135.390 1940 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.02 % Allowed : 17.26 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.27), residues: 1012 helix: 1.81 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.32 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.020 0.002 PHE A 420 TYR 0.009 0.001 TYR B 33 ARG 0.003 0.000 ARG B 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.868 Fit side-chains REVERT: A 161 MET cc_start: 0.8532 (mtp) cc_final: 0.8099 (mtm) REVERT: A 172 LEU cc_start: 0.7858 (tp) cc_final: 0.7433 (mt) REVERT: A 251 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6685 (pt) REVERT: A 381 SER cc_start: 0.7857 (m) cc_final: 0.7457 (p) REVERT: A 452 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: A 476 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 550 MET cc_start: 0.3653 (tpt) cc_final: 0.3065 (tpt) REVERT: B 119 LYS cc_start: 0.7289 (pttp) cc_final: 0.6980 (mtmm) REVERT: B 172 LEU cc_start: 0.7886 (tp) cc_final: 0.7463 (mt) REVERT: B 251 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.7011 (pt) REVERT: B 381 SER cc_start: 0.7844 (m) cc_final: 0.7475 (p) REVERT: B 452 MET cc_start: 0.8309 (mmp) cc_final: 0.8073 (mmm) REVERT: B 476 GLU cc_start: 0.7987 (tp30) cc_final: 0.7323 (mp0) outliers start: 17 outliers final: 9 residues processed: 121 average time/residue: 1.1610 time to fit residues: 150.3125 Evaluate side-chains 125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.151337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116962 restraints weight = 8106.193| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.16 r_work: 0.3098 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8488 Z= 0.216 Angle : 0.626 7.760 11588 Z= 0.303 Chirality : 0.042 0.138 1422 Planarity : 0.005 0.044 1352 Dihedral : 12.064 135.084 1940 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.02 % Allowed : 17.02 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 1012 helix: 1.70 (0.19), residues: 678 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.020 0.002 PHE A 420 TYR 0.010 0.001 TYR A 42 ARG 0.004 0.000 ARG B 456 =============================================================================== Job complete usr+sys time: 3116.52 seconds wall clock time: 56 minutes 56.56 seconds (3416.56 seconds total)