Starting phenix.real_space_refine on Tue Mar 11 20:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.map" model { file = "/net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vke_43315/03_2025/8vke_43315.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4218 2.51 5 N 1114 2.21 5 O 1290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6652 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "B" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "C" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.33, per 1000 atoms: 1.55 Number of scatterers: 6652 At special positions: 0 Unit cell: (81.78, 88.36, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1290 8.00 N 1114 7.00 C 4218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " " NAG R1301 " - " ASN R 343 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 20 sheets defined 12.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100A No H-bonds generated for 'chain 'H' and resid 99 through 100A' Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.616A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 372 removed outlier: 3.756A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 410 removed outlier: 3.687A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN R 409 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 99 through 100A No H-bonds generated for 'chain 'A' and resid 99 through 100A' Processing helix chain 'B' and resid 27A through 30 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.575A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.566A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.796A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.751A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.981A pdb=" N VAL H 35A" --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA H 96 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE H 100K" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.322A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'R' and resid 391 through 392 removed outlier: 3.861A pdb=" N PHE R 392 " --> pdb=" O VAL R 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL R 524 " --> pdb=" O PHE R 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.915A pdb=" N VAL A 35A" --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 50 " --> pdb=" O VAL A 35A" (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.054A pdb=" N ASN A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA A 96 " --> pdb=" O PHE A 100K" (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 100K" --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100C through 100E Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.330A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AB8, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.766A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474 248 hydrogen bonds defined for protein. 558 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: 2.14 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2123 1.35 - 1.48: 1885 1.48 - 1.60: 2772 1.60 - 1.72: 0 1.72 - 1.85: 36 Bond restraints: 6816 Sorted by residual: bond pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" C GLN B 6 " pdb=" N PRO B 7 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.35e+00 bond pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.97e+00 bond pdb=" N CYS R 480 " pdb=" CA CYS R 480 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N LYS R 478 " pdb=" CA LYS R 478 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.45e-02 4.76e+03 4.34e+00 ... (remaining 6811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8977 1.49 - 2.98: 260 2.98 - 4.47: 31 4.47 - 5.95: 1 5.95 - 7.44: 1 Bond angle restraints: 9270 Sorted by residual: angle pdb=" CA VAL B 11 " pdb=" C VAL B 11 " pdb=" O VAL B 11 " ideal model delta sigma weight residual 121.67 118.17 3.50 1.05e+00 9.07e-01 1.11e+01 angle pdb=" CA CYS R 391 " pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " ideal model delta sigma weight residual 114.40 121.84 -7.44 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA SER B 9 " pdb=" C SER B 9 " pdb=" O SER B 9 " ideal model delta sigma weight residual 121.23 118.05 3.18 1.07e+00 8.73e-01 8.85e+00 angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 107.15 3.55 1.22e+00 6.72e-01 8.48e+00 angle pdb=" O GLN B 6 " pdb=" C GLN B 6 " pdb=" N PRO B 7 " ideal model delta sigma weight residual 121.55 119.38 2.17 7.80e-01 1.64e+00 7.76e+00 ... (remaining 9265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3642 17.11 - 34.22: 308 34.22 - 51.33: 79 51.33 - 68.45: 16 68.45 - 85.56: 11 Dihedral angle restraints: 4056 sinusoidal: 1588 harmonic: 2468 Sorted by residual: dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.41 -75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 161.94 -68.94 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -38.05 -47.95 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 4053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 693 0.037 - 0.074: 217 0.074 - 0.111: 78 0.111 - 0.148: 31 0.148 - 0.185: 3 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA VAL B 11 " pdb=" N VAL B 11 " pdb=" C VAL B 11 " pdb=" CB VAL B 11 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ASN B 52 " pdb=" N ASN B 52 " pdb=" C ASN B 52 " pdb=" CB ASN B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1019 not shown) Planarity restraints: 1194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO C 479 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO C 373 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C VAL C 362 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL C 362 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA C 363 " 0.007 2.00e-02 2.50e+03 ... (remaining 1191 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 111 2.66 - 3.22: 5977 3.22 - 3.78: 10000 3.78 - 4.34: 14631 4.34 - 4.90: 24437 Nonbonded interactions: 55156 Sorted by model distance: nonbonded pdb=" O SER C 366 " pdb=" ND2 ASN C 370 " model vdw 2.103 3.120 nonbonded pdb=" O PHE R 486 " pdb=" ND2 ASN C 450 " model vdw 2.240 3.120 nonbonded pdb=" O TRP R 353 " pdb=" NH1 ARG R 466 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG H 71 " pdb=" OG1 THR H 73 " model vdw 2.281 3.120 nonbonded pdb=" N GLN H 105 " pdb=" OE1 GLN H 105 " model vdw 2.294 3.120 ... (remaining 55151 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'R' } 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: 19.690 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.003 0.050 6816 Z= 0.224 Angle : 0.591 7.443 9270 Z= 0.349 Chirality : 0.045 0.185 1022 Planarity : 0.004 0.078 1192 Dihedral : 14.192 85.558 2448 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.14 % Allowed : 13.86 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 838 helix: -3.52 (0.46), residues: 64 sheet: 1.18 (0.33), residues: 276 loop : -0.22 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS C 505 PHE 0.013 0.001 PHE R 392 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.772 Fit side-chains REVERT: L 17 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7062 (tt0) REVERT: L 78 LEU cc_start: 0.7864 (tp) cc_final: 0.7593 (mt) REVERT: R 466 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7887 (ptt180) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.1926 time to fit residues: 27.9160 Evaluate side-chains 105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN C 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108107 restraints weight = 8278.579| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.92 r_work: 0.3039 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6816 Z= 0.339 Angle : 0.608 7.707 9270 Z= 0.328 Chirality : 0.048 0.174 1022 Planarity : 0.005 0.050 1192 Dihedral : 5.968 53.091 980 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 13.04 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 838 helix: -3.91 (0.43), residues: 54 sheet: 0.90 (0.32), residues: 274 loop : -0.46 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS B 34 PHE 0.013 0.002 PHE R 392 TYR 0.027 0.002 TYR L 49 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.711 Fit side-chains REVERT: L 17 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7054 (tt0) REVERT: L 69 THR cc_start: 0.9086 (t) cc_final: 0.8545 (m) REVERT: L 78 LEU cc_start: 0.7966 (tp) cc_final: 0.7599 (mt) REVERT: A 56 GLU cc_start: 0.8632 (mp0) cc_final: 0.8412 (mt-10) REVERT: C 370 ASN cc_start: 0.7858 (m-40) cc_final: 0.7650 (m110) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 0.2057 time to fit residues: 30.0794 Evaluate side-chains 110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.138425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109630 restraints weight = 8240.672| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.94 r_work: 0.3086 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6816 Z= 0.218 Angle : 0.525 7.741 9270 Z= 0.284 Chirality : 0.045 0.169 1022 Planarity : 0.004 0.039 1192 Dihedral : 5.632 53.037 978 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 14.54 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 838 helix: -3.63 (0.52), residues: 50 sheet: 0.77 (0.31), residues: 278 loop : -0.56 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS B 34 PHE 0.008 0.001 PHE B 91 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG R 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.716 Fit side-chains REVERT: H 76 SER cc_start: 0.8432 (m) cc_final: 0.8067 (p) REVERT: L 17 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6991 (tt0) REVERT: L 69 THR cc_start: 0.9091 (t) cc_final: 0.8580 (m) REVERT: L 78 LEU cc_start: 0.7925 (tp) cc_final: 0.7577 (mt) REVERT: A 56 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: C 370 ASN cc_start: 0.8037 (m-40) cc_final: 0.7765 (m110) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.1975 time to fit residues: 30.6659 Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.135935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106858 restraints weight = 8227.210| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.98 r_work: 0.3049 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6816 Z= 0.262 Angle : 0.533 6.386 9270 Z= 0.288 Chirality : 0.045 0.169 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.636 52.812 978 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.12 % Allowed : 14.67 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 838 helix: -3.57 (0.55), residues: 50 sheet: 0.69 (0.31), residues: 278 loop : -0.63 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS B 34 PHE 0.009 0.001 PHE B 91 TYR 0.021 0.002 TYR L 49 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.791 Fit side-chains REVERT: H 76 SER cc_start: 0.8399 (m) cc_final: 0.8048 (p) REVERT: L 17 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6946 (tt0) REVERT: L 69 THR cc_start: 0.9167 (t) cc_final: 0.8698 (m) REVERT: L 78 LEU cc_start: 0.7928 (tp) cc_final: 0.7603 (mt) REVERT: A 56 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: C 370 ASN cc_start: 0.8137 (m-40) cc_final: 0.7820 (m110) REVERT: C 501 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8154 (m-10) outliers start: 23 outliers final: 17 residues processed: 123 average time/residue: 0.2145 time to fit residues: 34.6841 Evaluate side-chains 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.0030 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.137596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108695 restraints weight = 8151.024| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.94 r_work: 0.3077 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6816 Z= 0.231 Angle : 0.515 5.529 9270 Z= 0.279 Chirality : 0.045 0.170 1022 Planarity : 0.004 0.031 1192 Dihedral : 5.582 52.755 978 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.40 % Allowed : 14.81 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 838 helix: -3.73 (0.50), residues: 54 sheet: 0.64 (0.32), residues: 278 loop : -0.59 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS B 34 PHE 0.009 0.001 PHE C 486 TYR 0.019 0.002 TYR L 49 ARG 0.002 0.000 ARG R 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.764 Fit side-chains REVERT: H 76 SER cc_start: 0.8388 (m) cc_final: 0.8074 (p) REVERT: L 17 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7000 (tt0) REVERT: L 69 THR cc_start: 0.9155 (t) cc_final: 0.8683 (m) REVERT: L 78 LEU cc_start: 0.7857 (tp) cc_final: 0.7571 (mt) REVERT: A 56 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: C 370 ASN cc_start: 0.8203 (m-40) cc_final: 0.7800 (m-40) REVERT: C 501 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8114 (m-10) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.2033 time to fit residues: 31.8491 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN A 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110855 restraints weight = 8090.568| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.97 r_work: 0.3116 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6816 Z= 0.189 Angle : 0.496 6.062 9270 Z= 0.268 Chirality : 0.044 0.167 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.480 52.897 978 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.53 % Allowed : 15.08 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 838 helix: -3.80 (0.48), residues: 54 sheet: 0.86 (0.33), residues: 248 loop : -0.68 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 PHE 0.010 0.001 PHE C 486 TYR 0.016 0.001 TYR L 49 ARG 0.003 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.711 Fit side-chains REVERT: L 17 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7067 (tt0) REVERT: L 69 THR cc_start: 0.9102 (t) cc_final: 0.8614 (m) REVERT: L 78 LEU cc_start: 0.7913 (tp) cc_final: 0.7672 (mt) REVERT: R 409 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8878 (pt0) REVERT: A 56 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: A 82 ASN cc_start: 0.8379 (t0) cc_final: 0.8166 (m-40) REVERT: C 370 ASN cc_start: 0.8228 (m-40) cc_final: 0.7841 (m110) REVERT: C 501 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8081 (m-10) outliers start: 26 outliers final: 19 residues processed: 121 average time/residue: 0.2124 time to fit residues: 33.2436 Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 409 GLN Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.139430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112344 restraints weight = 8129.106| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.00 r_work: 0.3151 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6816 Z= 0.168 Angle : 0.495 4.962 9270 Z= 0.267 Chirality : 0.043 0.165 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.410 52.906 978 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.12 % Allowed : 15.35 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 838 helix: -3.80 (0.47), residues: 54 sheet: 0.87 (0.33), residues: 248 loop : -0.62 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 PHE 0.010 0.001 PHE C 486 TYR 0.015 0.001 TYR L 49 ARG 0.003 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.729 Fit side-chains REVERT: H 64 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7576 (tptm) REVERT: L 17 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7086 (tt0) REVERT: L 78 LEU cc_start: 0.7915 (tp) cc_final: 0.7707 (mt) REVERT: A 56 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: C 370 ASN cc_start: 0.8238 (m-40) cc_final: 0.7858 (m110) REVERT: C 501 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8017 (m-10) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.2139 time to fit residues: 32.2084 Evaluate side-chains 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103990 restraints weight = 8136.347| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.16 r_work: 0.2994 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6816 Z= 0.319 Angle : 0.566 4.830 9270 Z= 0.306 Chirality : 0.046 0.171 1022 Planarity : 0.004 0.040 1192 Dihedral : 5.674 52.509 978 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.67 % Allowed : 15.08 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 838 helix: -3.90 (0.47), residues: 54 sheet: 0.77 (0.33), residues: 248 loop : -0.76 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.010 0.001 PHE C 486 TYR 0.023 0.002 TYR B 49 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.709 Fit side-chains REVERT: H 64 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7204 (tptm) REVERT: L 17 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6690 (tt0) REVERT: L 78 LEU cc_start: 0.7717 (tp) cc_final: 0.7434 (mt) REVERT: A 56 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: C 501 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8077 (m-10) outliers start: 27 outliers final: 20 residues processed: 120 average time/residue: 0.2063 time to fit residues: 32.0751 Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 12 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106710 restraints weight = 8143.229| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.16 r_work: 0.3033 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6816 Z= 0.174 Angle : 0.509 4.474 9270 Z= 0.274 Chirality : 0.044 0.167 1022 Planarity : 0.004 0.035 1192 Dihedral : 5.551 52.860 978 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.12 % Allowed : 16.03 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 838 helix: -3.50 (0.45), residues: 66 sheet: 0.73 (0.33), residues: 248 loop : -0.59 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 PHE 0.010 0.001 PHE C 486 TYR 0.015 0.001 TYR L 49 ARG 0.004 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.731 Fit side-chains REVERT: H 64 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7188 (tptm) REVERT: L 17 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6672 (tt0) REVERT: L 78 LEU cc_start: 0.7641 (tp) cc_final: 0.7434 (mt) REVERT: A 56 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: A 58 SER cc_start: 0.8602 (t) cc_final: 0.8387 (m) REVERT: C 501 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7883 (m-10) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.2140 time to fit residues: 32.2605 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 52 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.135740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105221 restraints weight = 8308.685| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.16 r_work: 0.3056 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6816 Z= 0.223 Angle : 0.524 5.948 9270 Z= 0.283 Chirality : 0.044 0.168 1022 Planarity : 0.004 0.033 1192 Dihedral : 5.541 52.858 978 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.12 % Allowed : 16.17 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 838 helix: -3.51 (0.46), residues: 66 sheet: 0.76 (0.33), residues: 248 loop : -0.59 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS L 34 PHE 0.009 0.001 PHE C 486 TYR 0.020 0.001 TYR L 49 ARG 0.004 0.000 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.650 Fit side-chains REVERT: H 64 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7329 (tptm) REVERT: L 17 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6697 (tt0) REVERT: L 78 LEU cc_start: 0.7720 (tp) cc_final: 0.7496 (mt) REVERT: A 56 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: A 58 SER cc_start: 0.8638 (t) cc_final: 0.8419 (m) REVERT: C 501 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8037 (m-10) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.2064 time to fit residues: 31.9766 Evaluate side-chains 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105920 restraints weight = 8126.712| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.24 r_work: 0.3034 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6816 Z= 0.264 Angle : 0.543 7.411 9270 Z= 0.293 Chirality : 0.045 0.171 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.609 52.740 978 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.58 % Allowed : 16.58 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 838 helix: -3.52 (0.46), residues: 66 sheet: 0.73 (0.34), residues: 248 loop : -0.66 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS B 34 PHE 0.009 0.001 PHE C 486 TYR 0.021 0.002 TYR L 49 ARG 0.004 0.000 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.14 seconds wall clock time: 78 minutes 42.75 seconds (4722.75 seconds total)