Starting phenix.real_space_refine on Wed Mar 12 21:11:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204.map" model { file = "/net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jez_36204/03_2025/8jez_36204_neut.cif" } resolution = 2.6 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= 0.013 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 2 5.49 5 S 58 5.16 5 C 5508 2.51 5 N 1248 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3883 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 230 Unusual residues: {'AV0': 2, 'CLR': 2, 'LBN': 1, 'PLM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PLM:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, D Time building chain proxies: 8.16, per 1000 atoms: 0.99 Number of scatterers: 8282 At special positions: 0 Unit cell: (76.692, 108.564, 77.688, 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 58 16.00 P 2 15.00 O 1466 8.00 N 1248 7.00 C 5508 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 Atom "HETATM 8036 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3895 O5 NAG B 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 1 " - " ASN A 144 " " NAG D 1 " - " ASN C 144 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 74.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 3.914A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 75 through 101 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 145 through 173 Proline residue: A 151 - end of helix removed outlier: 3.543A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.851A pdb=" N ASN A 181 " --> pdb=" O GLY A 177 " (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 250 through 255 removed outlier: 3.621A pdb=" N MET A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) 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: 4.202A pdb=" N SER A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.306A 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 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.783A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.631A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 478 Proline residue: A 472 - end of helix 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 removed outlier: 3.508A pdb=" N LYS A 560 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 70 removed outlier: 3.914A pdb=" N SER C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 75 through 101 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 145 through 173 Proline residue: C 151 - end of helix removed outlier: 3.543A pdb=" N VAL C 166 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.851A pdb=" N ASN C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Proline residue: C 190 - end of helix Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 210 through 227 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.621A pdb=" N MET C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 274 Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 317 through 346 removed outlier: 4.202A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 374 Processing helix chain 'C' and resid 382 through 393 Processing helix chain 'C' and resid 396 through 413 removed outlier: 3.783A pdb=" N VAL C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.631A pdb=" N THR C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 Processing helix chain 'C' and resid 454 through 478 Proline residue: C 472 - end of helix Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 499 through 515 Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.508A pdb=" N LYS C 560 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=2, first strand: chain 'C' and resid 108 through 109 518 hydrogen bonds defined for protein. 1494 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: 2.27 Time building geometry restraints manager: 2.93 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: 1198 1.30 - 1.44: 2218 1.44 - 1.57: 4984 1.57 - 1.71: 8 1.71 - 1.85: 88 Bond restraints: 8496 Sorted by residual: bond pdb=" C MET A 161 " pdb=" O MET A 161 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.15e-02 7.56e+03 4.31e+01 bond pdb=" C MET C 161 " pdb=" O MET C 161 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.15e-02 7.56e+03 4.31e+01 bond pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.65e+01 bond pdb=" C VAL C 169 " pdb=" O VAL C 169 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.65e+01 bond pdb=" C LEU A 329 " pdb=" O LEU A 329 " ideal model delta sigma weight residual 1.237 1.300 -0.063 1.19e-02 7.06e+03 2.80e+01 ... (remaining 8491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 10164 2.77 - 5.53: 1394 5.53 - 8.30: 38 8.30 - 11.07: 2 11.07 - 13.83: 2 Bond angle restraints: 11600 Sorted by residual: angle pdb=" CA VAL C 353 " pdb=" C VAL C 353 " pdb=" O VAL C 353 " ideal model delta sigma weight residual 121.05 114.79 6.26 1.04e+00 9.25e-01 3.63e+01 angle pdb=" CA VAL A 353 " pdb=" C VAL A 353 " pdb=" O VAL A 353 " ideal model delta sigma weight residual 121.05 114.79 6.26 1.04e+00 9.25e-01 3.63e+01 angle pdb=" N LEU A 524 " pdb=" CA LEU A 524 " pdb=" C LEU A 524 " ideal model delta sigma weight residual 111.82 105.25 6.57 1.16e+00 7.43e-01 3.21e+01 angle pdb=" N LEU C 524 " pdb=" CA LEU C 524 " pdb=" C LEU C 524 " ideal model delta sigma weight residual 111.82 105.25 6.57 1.16e+00 7.43e-01 3.21e+01 angle pdb=" N VAL C 276 " pdb=" CA VAL C 276 " pdb=" C VAL C 276 " ideal model delta sigma weight residual 111.00 104.90 6.10 1.09e+00 8.42e-01 3.13e+01 ... (remaining 11595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 5312 29.34 - 58.69: 144 58.69 - 88.03: 28 88.03 - 117.37: 18 117.37 - 146.72: 10 Dihedral angle restraints: 5512 sinusoidal: 2606 harmonic: 2906 Sorted by residual: dihedral pdb=" C1 LBN A 602 " pdb=" O1 LBN A 602 " pdb=" P1 LBN A 602 " pdb=" O3 LBN A 602 " ideal model delta sinusoidal sigma weight residual -84.60 62.12 -146.72 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C1 LBN C 602 " pdb=" O1 LBN C 602 " pdb=" P1 LBN C 602 " pdb=" O3 LBN C 602 " ideal model delta sinusoidal sigma weight residual -84.60 62.12 -146.72 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" CCD AV0 A 603 " pdb=" CCS AV0 A 603 " pdb=" OBZ AV0 A 603 " pdb=" OCB AV0 A 603 " ideal model delta sinusoidal sigma weight residual 298.59 166.03 132.56 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1372 0.183 - 0.365: 58 0.365 - 0.547: 0 0.547 - 0.730: 0 0.730 - 0.912: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.31 0.91 2.00e-02 2.50e+03 2.08e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.31 0.91 2.00e-02 2.50e+03 2.08e+03 chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1429 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.358 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG B 2 " 0.117 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.358 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG D 2 " 0.117 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.330 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B 1 " -0.105 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.211 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2006 2.84 - 3.35: 8852 3.35 - 3.87: 14738 3.87 - 4.38: 17431 4.38 - 4.90: 28567 Nonbonded interactions: 71594 Sorted by model distance: nonbonded pdb=" O ILE C 160 " pdb=" OG SER C 164 " model vdw 2.325 3.040 nonbonded pdb=" O ILE A 160 " pdb=" OG SER A 164 " model vdw 2.325 3.040 nonbonded pdb=" O ILE A 510 " pdb=" OG1 THR A 514 " model vdw 2.373 3.040 nonbonded pdb=" O ILE C 510 " pdb=" OG1 THR C 514 " model vdw 2.373 3.040 nonbonded pdb=" O VAL C 460 " pdb=" OG SER C 464 " model vdw 2.445 3.040 ... (remaining 71589 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.420 Find NCS groups from input model: 0.150 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.016 0.084 8496 Z= 1.031 Angle : 1.786 13.833 11600 Z= 1.298 Chirality : 0.096 0.912 1432 Planarity : 0.020 0.309 1354 Dihedral : 17.037 146.716 3656 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.48 % Allowed : 4.76 % Favored : 94.76 % 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: -0.01 (0.25), residues: 1014 helix: 0.18 (0.18), residues: 674 sheet: -3.79 (1.03), residues: 20 loop : 0.23 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.010 TRP A 127 HIS 0.012 0.006 HIS C 147 PHE 0.049 0.010 PHE A 502 TYR 0.039 0.010 TYR C 227 ARG 0.023 0.003 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.895 Fit side-chains REVERT: A 181 ASN cc_start: 0.8570 (m-40) cc_final: 0.8348 (m-40) REVERT: A 229 ARG cc_start: 0.7455 (ptm160) cc_final: 0.5998 (ptt-90) REVERT: A 325 PHE cc_start: 0.7778 (t80) cc_final: 0.7576 (t80) REVERT: A 381 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 393 LYS cc_start: 0.7428 (mmtp) cc_final: 0.7115 (mptt) REVERT: A 465 MET cc_start: 0.8754 (mtp) cc_final: 0.8539 (mtm) REVERT: A 488 GLU cc_start: 0.6727 (tt0) cc_final: 0.5627 (mp0) REVERT: A 545 ASP cc_start: 0.7131 (m-30) cc_final: 0.6911 (m-30) REVERT: A 552 ILE cc_start: 0.5865 (mm) cc_final: 0.5595 (mp) REVERT: A 561 TYR cc_start: 0.5500 (m-80) cc_final: 0.5104 (m-80) REVERT: A 565 CYS cc_start: 0.6931 (m) cc_final: 0.6133 (t) REVERT: C 181 ASN cc_start: 0.8571 (m-40) cc_final: 0.8349 (m-40) REVERT: C 229 ARG cc_start: 0.7453 (ptm160) cc_final: 0.5999 (ptt-90) REVERT: C 325 PHE cc_start: 0.7782 (t80) cc_final: 0.7581 (t80) REVERT: C 381 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8082 (p) REVERT: C 393 LYS cc_start: 0.7426 (mmtp) cc_final: 0.7114 (mptt) REVERT: C 465 MET cc_start: 0.8754 (mtp) cc_final: 0.8538 (mtm) REVERT: C 488 GLU cc_start: 0.6726 (tt0) cc_final: 0.5625 (mp0) REVERT: C 545 ASP cc_start: 0.7133 (m-30) cc_final: 0.6912 (m-30) REVERT: C 552 ILE cc_start: 0.5870 (mm) cc_final: 0.5599 (mp) REVERT: C 561 TYR cc_start: 0.5501 (m-80) cc_final: 0.5102 (m-80) REVERT: C 565 CYS cc_start: 0.6931 (m) cc_final: 0.6132 (t) outliers start: 4 outliers final: 0 residues processed: 150 average time/residue: 1.1166 time to fit residues: 179.1594 Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 181 ASN A 287 GLN C 76 GLN C 181 ASN C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120787 restraints weight = 8662.692| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.34 r_work: 0.3206 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8496 Z= 0.202 Angle : 0.658 6.933 11600 Z= 0.320 Chirality : 0.045 0.250 1432 Planarity : 0.005 0.034 1354 Dihedral : 15.144 130.585 1954 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.67 % Allowed : 9.76 % Favored : 88.57 % 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: 1.89 (0.26), residues: 1014 helix: 1.55 (0.19), residues: 694 sheet: None (None), residues: 0 loop : 0.82 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 41 HIS 0.002 0.001 HIS C 354 PHE 0.015 0.002 PHE A 361 TYR 0.009 0.001 TYR A 402 ARG 0.007 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.847 Fit side-chains REVERT: A 32 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7060 (tp) REVERT: A 255 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7690 (p90) REVERT: A 262 MET cc_start: 0.7968 (mmm) cc_final: 0.7462 (mpt) REVERT: A 269 TYR cc_start: 0.7866 (t80) cc_final: 0.7643 (t80) REVERT: A 488 GLU cc_start: 0.7543 (tt0) cc_final: 0.6682 (mp0) REVERT: A 545 ASP cc_start: 0.7500 (m-30) cc_final: 0.7227 (m-30) REVERT: A 555 ARG cc_start: 0.7038 (mtm110) cc_final: 0.6117 (mtm180) REVERT: A 561 TYR cc_start: 0.5477 (m-80) cc_final: 0.5028 (m-80) REVERT: C 32 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7066 (tp) REVERT: C 255 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7679 (p90) REVERT: C 262 MET cc_start: 0.7961 (mmm) cc_final: 0.7458 (mpt) REVERT: C 269 TYR cc_start: 0.7861 (t80) cc_final: 0.7636 (t80) REVERT: C 488 GLU cc_start: 0.7534 (tt0) cc_final: 0.6671 (mp0) REVERT: C 545 ASP cc_start: 0.7512 (m-30) cc_final: 0.7240 (m-30) REVERT: C 555 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6107 (mtm180) REVERT: C 561 TYR cc_start: 0.5489 (m-80) cc_final: 0.5037 (m-80) outliers start: 14 outliers final: 2 residues processed: 142 average time/residue: 1.1217 time to fit residues: 170.2292 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN C 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126211 restraints weight = 8875.389| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.28 r_work: 0.3286 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8496 Z= 0.166 Angle : 0.589 7.454 11600 Z= 0.283 Chirality : 0.044 0.385 1432 Planarity : 0.004 0.036 1354 Dihedral : 13.663 126.865 1952 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.33 % Allowed : 10.48 % Favored : 86.19 % 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: 2.51 (0.26), residues: 1014 helix: 1.98 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 1.19 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS C 354 PHE 0.017 0.002 PHE A 558 TYR 0.007 0.001 TYR A 402 ARG 0.006 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.836 Fit side-chains REVERT: A 32 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7131 (tp) REVERT: A 251 ILE cc_start: 0.7010 (tt) cc_final: 0.6491 (tp) REVERT: A 262 MET cc_start: 0.8011 (mmm) cc_final: 0.7528 (mpt) REVERT: A 488 GLU cc_start: 0.7520 (tt0) cc_final: 0.6616 (mp0) REVERT: A 550 MET cc_start: 0.7225 (tpt) cc_final: 0.6724 (mmt) REVERT: A 561 TYR cc_start: 0.5486 (m-80) cc_final: 0.5062 (m-80) REVERT: C 32 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7138 (tp) REVERT: C 251 ILE cc_start: 0.7017 (tt) cc_final: 0.6500 (tp) REVERT: C 262 MET cc_start: 0.8014 (mmm) cc_final: 0.7530 (mpt) REVERT: C 488 GLU cc_start: 0.7523 (tt0) cc_final: 0.6620 (mp0) REVERT: C 550 MET cc_start: 0.7225 (tpt) cc_final: 0.6726 (mmt) REVERT: C 561 TYR cc_start: 0.5497 (m-80) cc_final: 0.5071 (m-80) outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.9798 time to fit residues: 156.4213 Evaluate side-chains 146 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 489 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119809 restraints weight = 8803.512| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.31 r_work: 0.3195 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8496 Z= 0.291 Angle : 0.686 7.523 11600 Z= 0.333 Chirality : 0.048 0.375 1432 Planarity : 0.005 0.047 1354 Dihedral : 13.764 133.678 1952 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.05 % Allowed : 11.19 % Favored : 84.76 % 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: 1.80 (0.26), residues: 1014 helix: 1.47 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.78 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 149 HIS 0.002 0.001 HIS C 354 PHE 0.020 0.002 PHE A 325 TYR 0.013 0.002 TYR A 340 ARG 0.009 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.919 Fit side-chains REVERT: A 250 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6991 (mm-40) REVERT: A 255 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6386 (p90) REVERT: A 262 MET cc_start: 0.8065 (mmm) cc_final: 0.7495 (mpt) REVERT: A 488 GLU cc_start: 0.7588 (tt0) cc_final: 0.6690 (mp0) REVERT: A 555 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6063 (mtm180) REVERT: C 250 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6998 (mm-40) REVERT: C 255 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6381 (p90) REVERT: C 262 MET cc_start: 0.8058 (mmm) cc_final: 0.7482 (mpt) REVERT: C 488 GLU cc_start: 0.7598 (tt0) cc_final: 0.6686 (mp0) REVERT: C 555 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6057 (mtm180) outliers start: 34 outliers final: 16 residues processed: 130 average time/residue: 1.1211 time to fit residues: 155.8658 Evaluate side-chains 130 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124513 restraints weight = 8718.238| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.30 r_work: 0.3260 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8496 Z= 0.173 Angle : 0.577 6.958 11600 Z= 0.281 Chirality : 0.043 0.349 1432 Planarity : 0.005 0.043 1354 Dihedral : 13.029 131.203 1952 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 12.86 % Favored : 84.29 % 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: 1014 helix: 1.73 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 1.14 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 149 HIS 0.001 0.000 HIS A 354 PHE 0.014 0.002 PHE A 558 TYR 0.008 0.001 TYR A 42 ARG 0.005 0.000 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.946 Fit side-chains REVERT: A 250 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: A 255 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6189 (p90) REVERT: A 262 MET cc_start: 0.8042 (mmm) cc_final: 0.7476 (mpt) REVERT: A 407 MET cc_start: 0.8558 (tpt) cc_final: 0.8201 (tpp) REVERT: A 488 GLU cc_start: 0.7583 (tt0) cc_final: 0.6671 (mp0) REVERT: A 550 MET cc_start: 0.7278 (tpt) cc_final: 0.6907 (mmt) REVERT: A 554 LYS cc_start: 0.6335 (mttt) cc_final: 0.6081 (mttt) REVERT: A 555 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6025 (mtm180) REVERT: C 250 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.7034 (mm-40) REVERT: C 255 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6193 (p90) REVERT: C 262 MET cc_start: 0.8044 (mmm) cc_final: 0.7473 (mpt) REVERT: C 407 MET cc_start: 0.8546 (tpt) cc_final: 0.8187 (tpp) REVERT: C 488 GLU cc_start: 0.7582 (tt0) cc_final: 0.6671 (mp0) REVERT: C 550 MET cc_start: 0.7285 (tpt) cc_final: 0.6918 (mmt) REVERT: C 554 LYS cc_start: 0.6334 (mttt) cc_final: 0.6080 (mttt) REVERT: C 555 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6010 (mtm180) outliers start: 24 outliers final: 14 residues processed: 133 average time/residue: 1.1530 time to fit residues: 164.2817 Evaluate side-chains 134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 A 287 GLN C 50 GLN C 76 GLN C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117173 restraints weight = 8744.297| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.37 r_work: 0.3148 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8496 Z= 0.321 Angle : 0.694 7.863 11600 Z= 0.338 Chirality : 0.048 0.320 1432 Planarity : 0.005 0.047 1354 Dihedral : 13.562 138.072 1952 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.05 % Allowed : 12.02 % Favored : 83.93 % 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: 1014 helix: 1.38 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.74 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 527 HIS 0.002 0.001 HIS C 147 PHE 0.017 0.002 PHE C 459 TYR 0.014 0.002 TYR A 340 ARG 0.005 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.933 Fit side-chains REVERT: A 250 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6997 (mm-40) REVERT: A 255 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6401 (p90) REVERT: A 262 MET cc_start: 0.8195 (mmm) cc_final: 0.7580 (mpt) REVERT: A 488 GLU cc_start: 0.7531 (tt0) cc_final: 0.6660 (mp0) REVERT: C 250 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6999 (mm-40) REVERT: C 255 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6393 (p90) REVERT: C 262 MET cc_start: 0.8199 (mmm) cc_final: 0.7579 (mpt) REVERT: C 488 GLU cc_start: 0.7532 (tt0) cc_final: 0.6659 (mp0) outliers start: 34 outliers final: 18 residues processed: 128 average time/residue: 1.1450 time to fit residues: 156.8101 Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.0070 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117909 restraints weight = 8801.036| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.38 r_work: 0.3160 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8496 Z= 0.284 Angle : 0.661 8.001 11600 Z= 0.324 Chirality : 0.046 0.283 1432 Planarity : 0.005 0.049 1354 Dihedral : 13.334 138.397 1952 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % 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: 1.65 (0.26), residues: 1014 helix: 1.27 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 0.94 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 149 HIS 0.002 0.001 HIS A 147 PHE 0.015 0.002 PHE A 459 TYR 0.012 0.002 TYR A 42 ARG 0.013 0.001 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.029 Fit side-chains REVERT: A 250 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6770 (mm-40) REVERT: A 255 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6362 (p90) REVERT: A 262 MET cc_start: 0.8185 (mmm) cc_final: 0.7553 (mpt) REVERT: A 407 MET cc_start: 0.8561 (tpt) cc_final: 0.8231 (tpp) REVERT: A 488 GLU cc_start: 0.7481 (tt0) cc_final: 0.6671 (mp0) REVERT: A 555 ARG cc_start: 0.7008 (mtm110) cc_final: 0.5994 (mtm180) REVERT: C 250 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6764 (mm-40) REVERT: C 255 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.6353 (p90) REVERT: C 262 MET cc_start: 0.8185 (mmm) cc_final: 0.7549 (mpt) REVERT: C 407 MET cc_start: 0.8550 (tpt) cc_final: 0.8218 (tpp) REVERT: C 488 GLU cc_start: 0.7489 (tt0) cc_final: 0.6671 (mp0) REVERT: C 555 ARG cc_start: 0.7004 (mtm110) cc_final: 0.5992 (mtm180) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 1.4021 time to fit residues: 185.3555 Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 0.0020 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118137 restraints weight = 8834.119| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.38 r_work: 0.3162 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8496 Z= 0.267 Angle : 0.648 7.923 11600 Z= 0.318 Chirality : 0.045 0.244 1432 Planarity : 0.005 0.047 1354 Dihedral : 13.233 139.362 1952 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % 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: 1.78 (0.26), residues: 1014 helix: 1.40 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.94 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 149 HIS 0.002 0.001 HIS C 147 PHE 0.015 0.002 PHE C 459 TYR 0.011 0.002 TYR A 42 ARG 0.010 0.001 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.060 Fit side-chains REVERT: A 250 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6701 (mm-40) REVERT: A 255 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.6369 (p90) REVERT: A 262 MET cc_start: 0.8188 (mmm) cc_final: 0.7596 (mpt) REVERT: A 407 MET cc_start: 0.8569 (tpt) cc_final: 0.8231 (tpp) REVERT: A 488 GLU cc_start: 0.7496 (tt0) cc_final: 0.6681 (mp0) REVERT: A 550 MET cc_start: 0.7175 (tpt) cc_final: 0.6770 (mmt) REVERT: A 554 LYS cc_start: 0.6220 (mtpt) cc_final: 0.5993 (mttt) REVERT: A 555 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6009 (mtm180) REVERT: C 250 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6687 (mm-40) REVERT: C 255 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6354 (p90) REVERT: C 262 MET cc_start: 0.8197 (mmm) cc_final: 0.7603 (mpt) REVERT: C 407 MET cc_start: 0.8557 (tpt) cc_final: 0.8218 (tpp) REVERT: C 488 GLU cc_start: 0.7502 (tt0) cc_final: 0.6686 (mp0) REVERT: C 550 MET cc_start: 0.7170 (tpt) cc_final: 0.6757 (mmt) REVERT: C 554 LYS cc_start: 0.6218 (mtpt) cc_final: 0.5995 (mttt) REVERT: C 555 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6003 (mtm180) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 1.2653 time to fit residues: 167.2981 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122041 restraints weight = 8997.454| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.39 r_work: 0.3219 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8496 Z= 0.169 Angle : 0.573 7.312 11600 Z= 0.284 Chirality : 0.041 0.200 1432 Planarity : 0.005 0.043 1354 Dihedral : 12.756 136.537 1952 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.79 % Allowed : 15.24 % Favored : 82.98 % 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: 2.14 (0.27), residues: 1014 helix: 1.63 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 1.19 (0.40), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.001 0.000 HIS A 354 PHE 0.015 0.002 PHE A 325 TYR 0.008 0.001 TYR C 402 ARG 0.008 0.001 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.371 Fit side-chains REVERT: A 250 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6717 (mm-40) REVERT: A 255 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6176 (p90) REVERT: A 262 MET cc_start: 0.8116 (mmm) cc_final: 0.7574 (mpt) REVERT: A 407 MET cc_start: 0.8612 (tpt) cc_final: 0.8252 (tpp) REVERT: A 488 GLU cc_start: 0.7568 (tt0) cc_final: 0.6711 (mp0) REVERT: A 550 MET cc_start: 0.7152 (tpt) cc_final: 0.6856 (mmt) REVERT: A 554 LYS cc_start: 0.6247 (mtpt) cc_final: 0.6027 (mttt) REVERT: A 555 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6016 (mtm180) REVERT: C 250 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6696 (mm-40) REVERT: C 255 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6174 (p90) REVERT: C 262 MET cc_start: 0.8123 (mmm) cc_final: 0.7576 (mpt) REVERT: C 407 MET cc_start: 0.8602 (tpt) cc_final: 0.8242 (tpp) REVERT: C 488 GLU cc_start: 0.7562 (tt0) cc_final: 0.6707 (mp0) REVERT: C 550 MET cc_start: 0.7158 (tpt) cc_final: 0.6863 (mmt) REVERT: C 554 LYS cc_start: 0.6251 (mtpt) cc_final: 0.6029 (mttt) REVERT: C 555 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6014 (mtm180) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 1.1918 time to fit residues: 165.2845 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 A 150 HIS A 287 GLN C 50 GLN C 76 GLN C 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119396 restraints weight = 8844.363| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.37 r_work: 0.3179 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8496 Z= 0.237 Angle : 0.621 7.720 11600 Z= 0.308 Chirality : 0.044 0.194 1432 Planarity : 0.005 0.044 1354 Dihedral : 12.907 140.086 1952 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.50 % Allowed : 14.52 % Favored : 82.98 % 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: 2.08 (0.26), residues: 1014 helix: 1.63 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 1.07 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 149 HIS 0.001 0.001 HIS A 147 PHE 0.014 0.002 PHE C 325 TYR 0.011 0.002 TYR A 307 ARG 0.008 0.001 ARG A 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.886 Fit side-chains REVERT: A 250 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6699 (mm-40) REVERT: A 255 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6323 (p90) REVERT: A 262 MET cc_start: 0.8139 (mmm) cc_final: 0.7551 (mpt) REVERT: A 407 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: A 488 GLU cc_start: 0.7572 (tt0) cc_final: 0.6735 (mp0) REVERT: A 550 MET cc_start: 0.7242 (tpt) cc_final: 0.6833 (mmt) REVERT: A 554 LYS cc_start: 0.6234 (mtpt) cc_final: 0.6015 (mttt) REVERT: A 555 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6013 (mtm180) REVERT: C 250 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6676 (mm-40) REVERT: C 255 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6317 (p90) REVERT: C 262 MET cc_start: 0.8151 (mmm) cc_final: 0.7560 (mpt) REVERT: C 407 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8247 (tpp) REVERT: C 488 GLU cc_start: 0.7569 (tt0) cc_final: 0.6742 (mp0) REVERT: C 550 MET cc_start: 0.7241 (tpt) cc_final: 0.6827 (mmt) REVERT: C 554 LYS cc_start: 0.6235 (mtpt) cc_final: 0.6016 (mttt) REVERT: C 555 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6003 (mtm180) outliers start: 21 outliers final: 12 residues processed: 118 average time/residue: 1.2284 time to fit residues: 154.4473 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 150 HIS C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120287 restraints weight = 8925.877| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.37 r_work: 0.3193 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8496 Z= 0.209 Angle : 0.605 7.589 11600 Z= 0.300 Chirality : 0.043 0.181 1432 Planarity : 0.005 0.044 1354 Dihedral : 12.835 139.545 1952 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 14.17 % Favored : 83.10 % 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: 2.11 (0.26), residues: 1014 helix: 1.62 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 1.15 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 149 HIS 0.002 0.001 HIS A 147 PHE 0.014 0.002 PHE C 325 TYR 0.017 0.002 TYR C 402 ARG 0.008 0.001 ARG C 555 =============================================================================== Job complete usr+sys time: 5561.21 seconds wall clock time: 97 minutes 24.32 seconds (5844.32 seconds total)