Starting phenix.real_space_refine on Tue May 13 15:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlf_27500/05_2025/8dlf_27500.cif" } resolution = 3.23 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4437 atoms to isotropic. 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 112 5.49 5 S 32 5.16 5 C 4224 2.51 5 N 1278 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7167 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "B" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1214 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "C" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1216 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "D" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1203 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1146 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "F" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1150 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.64 Number of scatterers: 7167 At special positions: 0 Unit cell: (80.205, 194.631, 72.7192, 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 32 16.00 P 112 15.00 O 1521 8.00 N 1278 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 738.3 milliseconds 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 5 sheets defined 35.0% alpha, 13.8% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.500A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 4.043A pdb=" N ALA A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.557A pdb=" N GLU A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 Processing helix chain 'B' and resid 513 through 528 Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.690A pdb=" N CYS B 591 " --> pdb=" O ALA B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 513 through 528 removed outlier: 3.636A pdb=" N ASN C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 Processing helix chain 'C' and resid 587 through 593 Processing helix chain 'D' and resid 475 through 490 Processing helix chain 'D' and resid 513 through 526 Processing helix chain 'D' and resid 568 through 586 removed outlier: 3.514A pdb=" N LEU D 575 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 614 removed outlier: 3.766A pdb=" N VAL D 614 " --> pdb=" O PRO D 611 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 505 through 510 removed outlier: 3.542A pdb=" N VAL A 509 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL A 559 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 532 through 533 removed outlier: 4.579A pdb=" N LEU B 539 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 559 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 537 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 removed outlier: 5.492A pdb=" N CYS B 560 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 506 " --> pdb=" O CYS B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.876A pdb=" N GLY C 506 " --> pdb=" O CYS C 598 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 537 through 540 removed outlier: 5.354A pdb=" N VAL D 559 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N CYS D 560 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 509 " --> pdb=" O PHE D 562 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1507 1.33 - 1.45: 2160 1.45 - 1.57: 3644 1.57 - 1.69: 222 1.69 - 1.81: 48 Bond restraints: 7581 Sorted by residual: bond pdb=" O3' DA E 39 " pdb=" P DG E 40 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.07e+01 bond pdb=" P DA E 54 " pdb=" OP1 DA E 54 " ideal model delta sigma weight residual 1.480 1.541 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" N GLY A 463 " pdb=" CA GLY A 463 " ideal model delta sigma weight residual 1.447 1.474 -0.027 9.90e-03 1.02e+04 7.18e+00 bond pdb=" O3' DT F 3 " pdb=" P DA F 4 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.93e+00 bond pdb=" N TRP A 464 " pdb=" CA TRP A 464 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.22e-02 6.72e+03 6.08e+00 ... (remaining 7576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 9608 1.66 - 3.31: 755 3.31 - 4.97: 178 4.97 - 6.62: 205 6.62 - 8.28: 21 Bond angle restraints: 10767 Sorted by residual: angle pdb=" C2' DT E 34 " pdb=" C1' DT E 34 " pdb=" N1 DT E 34 " ideal model delta sigma weight residual 113.50 121.78 -8.28 1.50e+00 4.44e-01 3.05e+01 angle pdb=" CA GLY A 463 " pdb=" C GLY A 463 " pdb=" O GLY A 463 " ideal model delta sigma weight residual 122.52 118.34 4.18 7.90e-01 1.60e+00 2.80e+01 angle pdb=" O3' DG E 16 " pdb=" P DC E 17 " pdb=" O5' DC E 17 " ideal model delta sigma weight residual 104.00 96.31 7.69 1.50e+00 4.44e-01 2.62e+01 angle pdb=" O3' DT F 33 " pdb=" P DA F 34 " pdb=" O5' DA F 34 " ideal model delta sigma weight residual 104.00 111.00 -7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C3' DT E 30 " pdb=" O3' DT E 30 " pdb=" P DA E 31 " ideal model delta sigma weight residual 120.20 113.70 6.50 1.50e+00 4.44e-01 1.88e+01 ... (remaining 10762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 3637 34.38 - 68.76: 581 68.76 - 103.15: 10 103.15 - 137.53: 3 137.53 - 171.91: 6 Dihedral angle restraints: 4237 sinusoidal: 2476 harmonic: 1761 Sorted by residual: dihedral pdb=" CA PHE C 610 " pdb=" C PHE C 610 " pdb=" N PRO C 611 " pdb=" CA PRO C 611 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C4' DC F 50 " pdb=" C3' DC F 50 " pdb=" O3' DC F 50 " pdb=" P DC F 51 " ideal model delta sinusoidal sigma weight residual 220.00 48.09 171.91 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG F 1 " pdb=" C3' DG F 1 " pdb=" O3' DG F 1 " pdb=" P DA F 2 " ideal model delta sinusoidal sigma weight residual 220.00 57.93 162.07 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 4234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1054 0.128 - 0.256: 16 0.256 - 0.384: 7 0.384 - 0.512: 65 0.512 - 0.641: 35 Chirality restraints: 1177 Sorted by residual: chirality pdb=" P DG F 40 " pdb=" OP1 DG F 40 " pdb=" OP2 DG F 40 " pdb=" O5' DG F 40 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG F 1 " pdb=" OP1 DG F 1 " pdb=" OP2 DG F 1 " pdb=" O5' DG F 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DA E 1 " pdb=" OP1 DA E 1 " pdb=" OP2 DA E 1 " pdb=" O5' DA E 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.74e+00 ... (remaining 1174 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 586 " 0.013 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C LYS D 586 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS D 586 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO D 587 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 611 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO B 612 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 612 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 612 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 611 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 612 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " -0.029 5.00e-02 4.00e+02 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 260 2.66 - 3.22: 6953 3.22 - 3.78: 14282 3.78 - 4.34: 17543 4.34 - 4.90: 25998 Nonbonded interactions: 65036 Sorted by model distance: nonbonded pdb=" ND2 ASN B 480 " pdb=" OP2 DT E 34 " model vdw 2.103 3.120 nonbonded pdb=" NH1 ARG C 538 " pdb=" O SER C 557 " model vdw 2.243 3.120 nonbonded pdb=" OG SER C 599 " pdb=" O SER D 599 " model vdw 2.255 3.040 nonbonded pdb=" O PRO C 476 " pdb=" ND2 ASN C 480 " model vdw 2.267 3.120 nonbonded pdb=" O LEU D 582 " pdb=" OG1 THR D 585 " model vdw 2.277 3.040 ... (remaining 65031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 461 through 614) selection = (chain 'B' and resid 461 through 614) selection = (chain 'C' and resid 461 through 614) selection = (chain 'D' and resid 461 through 614) } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.820 Find NCS groups from input model: 0.260 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4623 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 : 0.009 0.061 7581 Z= 0.413 Angle : 1.289 8.280 10767 Z= 0.656 Chirality : 0.156 0.641 1177 Planarity : 0.006 0.059 999 Dihedral : 25.899 171.910 3115 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 35.48 Ramachandran Plot: Outliers : 1.44 % Allowed : 8.35 % Favored : 90.21 % Rotamer: Outliers : 8.48 % Allowed : 10.02 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.34), residues: 623 helix: 1.15 (0.37), residues: 195 sheet: -2.01 (0.52), residues: 76 loop : -2.44 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 464 HIS 0.002 0.001 HIS A 493 PHE 0.017 0.002 PHE D 562 TYR 0.008 0.002 TYR C 518 ARG 0.004 0.000 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.20520 ( 289) hydrogen bonds : angle 11.08637 ( 726) covalent geometry : bond 0.00863 ( 7581) covalent geometry : angle 1.28878 (10767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.3676 (OUTLIER) cc_final: 0.3171 (m170) REVERT: A 495 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6629 (tt0) REVERT: A 602 ASP cc_start: 0.2129 (t0) cc_final: 0.1884 (p0) REVERT: B 497 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5633 (t) REVERT: B 565 PHE cc_start: 0.4431 (m-80) cc_final: 0.3271 (m-80) REVERT: C 497 THR cc_start: 0.6432 (OUTLIER) cc_final: 0.5872 (t) REVERT: C 562 PHE cc_start: 0.5176 (p90) cc_final: 0.4972 (p90) REVERT: C 565 PHE cc_start: 0.4890 (m-10) cc_final: 0.3896 (m-80) REVERT: D 467 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3833 (mmmt) outliers start: 44 outliers final: 17 residues processed: 178 average time/residue: 0.2283 time to fit residues: 51.5116 Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN D 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.225981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.205791 restraints weight = 12859.513| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 1.83 r_work: 0.4708 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7581 Z= 0.205 Angle : 0.785 12.538 10767 Z= 0.426 Chirality : 0.047 0.214 1177 Planarity : 0.007 0.058 999 Dihedral : 30.329 176.986 1975 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.47 % Favored : 89.57 % Rotamer: Outliers : 7.13 % Allowed : 14.45 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.34), residues: 623 helix: 0.82 (0.37), residues: 198 sheet: -2.16 (0.53), residues: 82 loop : -2.37 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 503 HIS 0.003 0.001 HIS A 468 PHE 0.026 0.002 PHE D 610 TYR 0.011 0.002 TYR B 518 ARG 0.003 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.07591 ( 289) hydrogen bonds : angle 5.40060 ( 726) covalent geometry : bond 0.00474 ( 7581) covalent geometry : angle 0.78533 (10767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5064 (OUTLIER) cc_final: 0.4326 (m170) REVERT: A 602 ASP cc_start: 0.3136 (t0) cc_final: 0.2881 (p0) REVERT: B 556 GLU cc_start: 0.3431 (OUTLIER) cc_final: 0.2701 (pm20) REVERT: B 558 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6972 (pp) REVERT: C 497 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.5942 (t) REVERT: C 562 PHE cc_start: 0.5429 (p90) cc_final: 0.5211 (p90) REVERT: C 565 PHE cc_start: 0.5130 (m-10) cc_final: 0.4731 (m-80) outliers start: 37 outliers final: 17 residues processed: 136 average time/residue: 0.1921 time to fit residues: 34.3975 Evaluate side-chains 112 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.218261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.198965 restraints weight = 13221.279| |-----------------------------------------------------------------------------| r_work (start): 0.4780 rms_B_bonded: 1.79 r_work: 0.4630 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7581 Z= 0.281 Angle : 0.859 14.412 10767 Z= 0.462 Chirality : 0.051 0.266 1177 Planarity : 0.008 0.064 999 Dihedral : 30.323 173.132 1957 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.43 % Favored : 88.44 % Rotamer: Outliers : 7.13 % Allowed : 17.53 % Favored : 75.34 % 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: -2.19 (0.33), residues: 623 helix: 0.11 (0.37), residues: 197 sheet: -1.98 (0.61), residues: 66 loop : -2.36 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 503 HIS 0.003 0.001 HIS C 569 PHE 0.021 0.003 PHE D 562 TYR 0.022 0.004 TYR D 510 ARG 0.007 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.08145 ( 289) hydrogen bonds : angle 5.72888 ( 726) covalent geometry : bond 0.00655 ( 7581) covalent geometry : angle 0.85914 (10767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.6049 (OUTLIER) cc_final: 0.5330 (m170) REVERT: A 602 ASP cc_start: 0.3205 (t0) cc_final: 0.2739 (p0) REVERT: B 556 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.4000 (pm20) REVERT: B 558 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6970 (pp) REVERT: C 497 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6047 (t) REVERT: C 543 MET cc_start: 0.2314 (OUTLIER) cc_final: 0.1437 (tmm) REVERT: C 565 PHE cc_start: 0.5399 (m-10) cc_final: 0.4458 (m-80) REVERT: D 543 MET cc_start: 0.4336 (mtt) cc_final: 0.3983 (mtt) REVERT: D 565 PHE cc_start: 0.2341 (OUTLIER) cc_final: -0.0000 (m-80) outliers start: 37 outliers final: 20 residues processed: 126 average time/residue: 0.2171 time to fit residues: 35.5093 Evaluate side-chains 106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.221428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.203162 restraints weight = 13165.561| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 1.75 r_work: 0.4681 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7581 Z= 0.196 Angle : 0.755 12.071 10767 Z= 0.408 Chirality : 0.046 0.196 1177 Planarity : 0.007 0.060 999 Dihedral : 30.436 174.502 1955 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.67 % Favored : 90.21 % Rotamer: Outliers : 7.32 % Allowed : 19.08 % Favored : 73.60 % 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: -2.27 (0.34), residues: 623 helix: 0.43 (0.37), residues: 193 sheet: -2.64 (0.53), residues: 77 loop : -2.47 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 609 HIS 0.002 0.001 HIS A 468 PHE 0.036 0.003 PHE D 610 TYR 0.015 0.002 TYR D 510 ARG 0.006 0.000 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.06413 ( 289) hydrogen bonds : angle 5.20106 ( 726) covalent geometry : bond 0.00458 ( 7581) covalent geometry : angle 0.75543 (10767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.5313 (mttt) cc_final: 0.5085 (mtmt) REVERT: A 468 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.5043 (m170) REVERT: A 584 MET cc_start: 0.3654 (tmm) cc_final: 0.3104 (mtt) REVERT: A 602 ASP cc_start: 0.3391 (t0) cc_final: 0.2840 (p0) REVERT: B 475 ASN cc_start: 0.3669 (OUTLIER) cc_final: 0.3266 (t0) REVERT: B 556 GLU cc_start: 0.3607 (OUTLIER) cc_final: 0.3143 (pm20) REVERT: B 558 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6928 (pp) REVERT: C 543 MET cc_start: 0.2243 (ttm) cc_final: 0.1921 (tmm) REVERT: C 565 PHE cc_start: 0.5198 (m-10) cc_final: 0.4721 (m-80) outliers start: 38 outliers final: 20 residues processed: 120 average time/residue: 0.1876 time to fit residues: 29.8582 Evaluate side-chains 109 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.225625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.208811 restraints weight = 13042.103| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 1.61 r_work: 0.4749 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7581 Z= 0.165 Angle : 0.700 10.024 10767 Z= 0.379 Chirality : 0.043 0.200 1177 Planarity : 0.007 0.063 999 Dihedral : 30.223 175.629 1953 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.31 % Favored : 89.89 % Rotamer: Outliers : 5.59 % Allowed : 19.65 % Favored : 74.76 % 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: -2.01 (0.34), residues: 623 helix: 0.61 (0.38), residues: 201 sheet: -2.64 (0.52), residues: 76 loop : -2.31 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 464 HIS 0.003 0.000 HIS A 468 PHE 0.019 0.002 PHE D 562 TYR 0.013 0.002 TYR D 510 ARG 0.005 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 289) hydrogen bonds : angle 4.94641 ( 726) covalent geometry : bond 0.00380 ( 7581) covalent geometry : angle 0.70047 (10767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.3300 (t0) cc_final: 0.2674 (p0) REVERT: B 475 ASN cc_start: 0.3543 (t0) cc_final: 0.3108 (t0) REVERT: B 558 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6972 (pp) REVERT: C 565 PHE cc_start: 0.4732 (m-10) cc_final: 0.4442 (m-80) REVERT: D 543 MET cc_start: 0.4222 (mtt) cc_final: 0.3788 (mtt) outliers start: 29 outliers final: 21 residues processed: 119 average time/residue: 0.1853 time to fit residues: 29.5954 Evaluate side-chains 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.223268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.205904 restraints weight = 13026.876| |-----------------------------------------------------------------------------| r_work (start): 0.4850 rms_B_bonded: 1.62 r_work: 0.4712 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7581 Z= 0.184 Angle : 0.726 10.908 10767 Z= 0.389 Chirality : 0.044 0.258 1177 Planarity : 0.007 0.060 999 Dihedral : 30.049 176.588 1951 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.95 % Favored : 89.25 % Rotamer: Outliers : 5.59 % Allowed : 20.23 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.34), residues: 623 helix: 0.61 (0.38), residues: 200 sheet: -2.45 (0.55), residues: 71 loop : -2.32 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 468 PHE 0.035 0.002 PHE D 610 TYR 0.016 0.002 TYR A 518 ARG 0.009 0.001 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05834 ( 289) hydrogen bonds : angle 5.01666 ( 726) covalent geometry : bond 0.00431 ( 7581) covalent geometry : angle 0.72582 (10767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5846 (OUTLIER) cc_final: 0.5183 (m-70) REVERT: A 602 ASP cc_start: 0.3256 (t0) cc_final: 0.2668 (p0) REVERT: B 556 GLU cc_start: 0.3619 (OUTLIER) cc_final: 0.3239 (pm20) REVERT: B 558 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6985 (pp) REVERT: C 565 PHE cc_start: 0.4927 (m-10) cc_final: 0.4538 (m-80) REVERT: D 543 MET cc_start: 0.4148 (mtt) cc_final: 0.3722 (mtt) outliers start: 29 outliers final: 21 residues processed: 105 average time/residue: 0.1844 time to fit residues: 25.9617 Evaluate side-chains 106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 41 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.224631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.207515 restraints weight = 12999.516| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 1.61 r_work: 0.4737 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7581 Z= 0.171 Angle : 0.710 10.827 10767 Z= 0.382 Chirality : 0.044 0.271 1177 Planarity : 0.007 0.063 999 Dihedral : 29.966 177.424 1951 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.79 % Favored : 89.41 % Rotamer: Outliers : 5.20 % Allowed : 20.81 % Favored : 73.99 % 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: -2.01 (0.34), residues: 623 helix: 0.65 (0.38), residues: 203 sheet: -2.67 (0.52), residues: 77 loop : -2.35 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 503 HIS 0.013 0.001 HIS A 468 PHE 0.018 0.002 PHE D 562 TYR 0.014 0.002 TYR A 518 ARG 0.005 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 289) hydrogen bonds : angle 4.84207 ( 726) covalent geometry : bond 0.00401 ( 7581) covalent geometry : angle 0.70966 (10767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4686 (OUTLIER) cc_final: 0.4268 (mt) REVERT: A 602 ASP cc_start: 0.3190 (t0) cc_final: 0.2565 (p0) REVERT: B 475 ASN cc_start: 0.3502 (OUTLIER) cc_final: 0.3086 (t0) REVERT: B 558 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.7014 (pp) REVERT: C 565 PHE cc_start: 0.4792 (m-10) cc_final: 0.3673 (m-80) REVERT: D 543 MET cc_start: 0.4087 (mtt) cc_final: 0.3839 (mtt) outliers start: 27 outliers final: 22 residues processed: 99 average time/residue: 0.1966 time to fit residues: 26.0690 Evaluate side-chains 104 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.224322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.205856 restraints weight = 13270.612| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 1.74 r_work: 0.4700 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7581 Z= 0.177 Angle : 0.714 10.247 10767 Z= 0.385 Chirality : 0.044 0.233 1177 Planarity : 0.007 0.065 999 Dihedral : 29.877 177.940 1951 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.11 % Favored : 89.09 % Rotamer: Outliers : 5.20 % Allowed : 21.58 % Favored : 73.22 % 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: -2.02 (0.34), residues: 623 helix: 0.76 (0.39), residues: 197 sheet: -2.68 (0.52), residues: 79 loop : -2.38 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 609 HIS 0.006 0.001 HIS A 468 PHE 0.036 0.002 PHE D 610 TYR 0.013 0.002 TYR A 518 ARG 0.004 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 289) hydrogen bonds : angle 4.86184 ( 726) covalent geometry : bond 0.00414 ( 7581) covalent geometry : angle 0.71399 (10767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5200 (m170) REVERT: A 526 LEU cc_start: 0.4404 (OUTLIER) cc_final: 0.4141 (mt) REVERT: A 602 ASP cc_start: 0.3043 (t0) cc_final: 0.2473 (p0) REVERT: B 475 ASN cc_start: 0.3640 (OUTLIER) cc_final: 0.3219 (t0) REVERT: B 556 GLU cc_start: 0.3616 (OUTLIER) cc_final: 0.3248 (pm20) REVERT: C 565 PHE cc_start: 0.4955 (m-10) cc_final: 0.4514 (m-80) outliers start: 27 outliers final: 19 residues processed: 102 average time/residue: 0.1782 time to fit residues: 24.7969 Evaluate side-chains 102 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.221287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.203521 restraints weight = 13187.677| |-----------------------------------------------------------------------------| r_work (start): 0.4822 rms_B_bonded: 1.65 r_work: 0.4679 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7581 Z= 0.207 Angle : 0.763 11.530 10767 Z= 0.409 Chirality : 0.046 0.246 1177 Planarity : 0.008 0.067 999 Dihedral : 29.896 177.760 1951 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.08 % Favored : 88.12 % Rotamer: Outliers : 4.82 % Allowed : 20.62 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.33), residues: 623 helix: 0.59 (0.39), residues: 195 sheet: -2.30 (0.57), residues: 66 loop : -2.50 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 609 HIS 0.004 0.001 HIS A 468 PHE 0.021 0.002 PHE B 610 TYR 0.014 0.002 TYR C 510 ARG 0.007 0.001 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 289) hydrogen bonds : angle 5.05608 ( 726) covalent geometry : bond 0.00486 ( 7581) covalent geometry : angle 0.76337 (10767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4289 (mt) REVERT: A 602 ASP cc_start: 0.3003 (t0) cc_final: 0.2397 (p0) REVERT: B 475 ASN cc_start: 0.3572 (OUTLIER) cc_final: 0.3140 (t0) REVERT: B 556 GLU cc_start: 0.3626 (OUTLIER) cc_final: 0.3245 (pm20) REVERT: C 565 PHE cc_start: 0.5095 (m-10) cc_final: 0.4586 (m-80) outliers start: 25 outliers final: 21 residues processed: 98 average time/residue: 0.1816 time to fit residues: 24.0191 Evaluate side-chains 101 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 0.0050 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.225791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.208448 restraints weight = 13493.789| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 1.65 r_work: 0.4736 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7581 Z= 0.165 Angle : 0.712 9.699 10767 Z= 0.384 Chirality : 0.044 0.266 1177 Planarity : 0.007 0.069 999 Dihedral : 29.773 179.210 1951 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.19 % Favored : 91.01 % Rotamer: Outliers : 4.43 % Allowed : 21.58 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.34), residues: 623 helix: 0.83 (0.39), residues: 198 sheet: -2.71 (0.51), residues: 79 loop : -2.39 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 609 HIS 0.006 0.001 HIS A 468 PHE 0.021 0.002 PHE B 610 TYR 0.017 0.002 TYR A 518 ARG 0.005 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 289) hydrogen bonds : angle 4.78247 ( 726) covalent geometry : bond 0.00385 ( 7581) covalent geometry : angle 0.71228 (10767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.3024 (t0) cc_final: 0.2176 (p0) REVERT: B 475 ASN cc_start: 0.3305 (OUTLIER) cc_final: 0.2862 (t0) REVERT: C 565 PHE cc_start: 0.4635 (m-80) cc_final: 0.3545 (m-80) outliers start: 23 outliers final: 20 residues processed: 99 average time/residue: 0.1886 time to fit residues: 25.1861 Evaluate side-chains 100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.0020 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 chunk 2 optimal weight: 0.7980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.222775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.205177 restraints weight = 13193.826| |-----------------------------------------------------------------------------| r_work (start): 0.4841 rms_B_bonded: 1.63 r_work: 0.4700 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7581 Z= 0.194 Angle : 0.744 10.734 10767 Z= 0.398 Chirality : 0.045 0.257 1177 Planarity : 0.007 0.069 999 Dihedral : 29.809 178.492 1949 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.43 % Favored : 88.76 % Rotamer: Outliers : 4.62 % Allowed : 21.00 % Favored : 74.37 % 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: -2.11 (0.34), residues: 623 helix: 0.73 (0.39), residues: 195 sheet: -2.66 (0.50), residues: 82 loop : -2.45 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 609 HIS 0.005 0.001 HIS A 468 PHE 0.022 0.002 PHE B 610 TYR 0.017 0.002 TYR A 518 ARG 0.004 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 289) hydrogen bonds : angle 4.93788 ( 726) covalent geometry : bond 0.00457 ( 7581) covalent geometry : angle 0.74391 (10767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.65 seconds wall clock time: 58 minutes 44.64 seconds (3524.64 seconds total)