Starting phenix.real_space_refine on Mon Jul 28 20:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlf_27500/07_2025/8dlf_27500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlf_27500/07_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_27500/07_2025/8dlf_27500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2025/8dlf_27500.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2025/8dlf_27500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_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-5711/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: 4.95, per 1000 atoms: 0.69 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: 1.81 Conformation dependent library (CDL) restraints added in 831.1 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: 3.40 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: 2.37 Time building geometry restraints manager: 2.15 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: 0.710 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.120 Find NCS groups from input model: 0.280 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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 : 0.657 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: 0.2378 time to fit residues: 53.7316 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 : 0.669 ------------------------------------------------------------------------------- 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 = 0.5064 r_free = 0.5064 target = 0.225965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.205738 restraints weight = 12855.356| |-----------------------------------------------------------------------------| r_work (start): 0.4850 rms_B_bonded: 1.84 r_work: 0.4707 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 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 : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5060 (OUTLIER) cc_final: 0.4316 (m170) REVERT: A 602 ASP cc_start: 0.3111 (t0) cc_final: 0.2856 (p0) REVERT: B 556 GLU cc_start: 0.3439 (OUTLIER) cc_final: 0.2709 (pm20) REVERT: B 558 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6958 (pp) REVERT: C 497 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.5940 (t) REVERT: C 562 PHE cc_start: 0.5426 (p90) cc_final: 0.5209 (p90) REVERT: C 565 PHE cc_start: 0.5130 (m-10) cc_final: 0.4732 (m-80) outliers start: 37 outliers final: 17 residues processed: 136 average time/residue: 0.2172 time to fit residues: 39.3640 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 : 0.592 ------------------------------------------------------------------------------- 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: 0.7980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.5001 r_free = 0.5001 target = 0.218899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.200408 restraints weight = 13279.434| |-----------------------------------------------------------------------------| r_work (start): 0.4794 rms_B_bonded: 1.69 r_work: 0.4650 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7581 Z= 0.268 Angle : 0.847 13.989 10767 Z= 0.456 Chirality : 0.050 0.253 1177 Planarity : 0.008 0.063 999 Dihedral : 30.299 173.253 1957 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.75 % Favored : 88.12 % Rotamer: Outliers : 7.13 % Allowed : 17.15 % Favored : 75.72 % 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: -2.20 (0.33), residues: 623 helix: 0.09 (0.37), residues: 199 sheet: -1.94 (0.62), residues: 66 loop : -2.38 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 503 HIS 0.003 0.001 HIS C 569 PHE 0.019 0.003 PHE D 562 TYR 0.022 0.004 TYR D 510 ARG 0.006 0.001 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.08030 ( 289) hydrogen bonds : angle 5.70222 ( 726) covalent geometry : bond 0.00628 ( 7581) covalent geometry : angle 0.84729 (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 : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5311 (m170) REVERT: A 602 ASP cc_start: 0.3209 (t0) cc_final: 0.2728 (p0) REVERT: B 556 GLU cc_start: 0.4464 (OUTLIER) cc_final: 0.3981 (pm20) REVERT: B 558 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6987 (pp) REVERT: C 497 THR cc_start: 0.6565 (OUTLIER) cc_final: 0.6072 (t) REVERT: C 543 MET cc_start: 0.2282 (OUTLIER) cc_final: 0.1433 (tmm) REVERT: C 565 PHE cc_start: 0.5354 (m-10) cc_final: 0.4438 (m-80) REVERT: D 543 MET cc_start: 0.4249 (mtt) cc_final: 0.3922 (mtt) REVERT: D 565 PHE cc_start: 0.2256 (OUTLIER) cc_final: -0.0093 (m-80) outliers start: 37 outliers final: 20 residues processed: 126 average time/residue: 0.2310 time to fit residues: 37.3794 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 : 0.643 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 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 = 0.221324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.203011 restraints weight = 13157.883| |-----------------------------------------------------------------------------| r_work (start): 0.4825 rms_B_bonded: 1.75 r_work: 0.4680 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7581 Z= 0.198 Angle : 0.757 12.275 10767 Z= 0.409 Chirality : 0.045 0.197 1177 Planarity : 0.007 0.060 999 Dihedral : 30.393 173.709 1955 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.67 % Favored : 90.21 % Rotamer: Outliers : 6.74 % Allowed : 19.85 % Favored : 73.41 % 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: -2.26 (0.34), residues: 623 helix: 0.43 (0.38), residues: 193 sheet: -2.64 (0.54), residues: 77 loop : -2.46 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 PHE 0.033 0.003 PHE D 610 TYR 0.015 0.002 TYR D 510 ARG 0.005 0.000 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.06467 ( 289) hydrogen bonds : angle 5.25777 ( 726) covalent geometry : bond 0.00465 ( 7581) covalent geometry : angle 0.75667 (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 127 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5765 (OUTLIER) cc_final: 0.5028 (m170) REVERT: A 584 MET cc_start: 0.3533 (tmm) cc_final: 0.3096 (mtt) REVERT: A 602 ASP cc_start: 0.3002 (t0) cc_final: 0.2627 (p0) REVERT: B 475 ASN cc_start: 0.3663 (t0) cc_final: 0.3261 (t0) REVERT: B 556 GLU cc_start: 0.3660 (OUTLIER) cc_final: 0.3152 (pm20) REVERT: B 558 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6961 (pp) REVERT: C 543 MET cc_start: 0.2349 (ttm) cc_final: 0.1992 (tmm) REVERT: C 565 PHE cc_start: 0.5216 (m-10) cc_final: 0.4674 (m-80) outliers start: 35 outliers final: 23 residues processed: 118 average time/residue: 0.2090 time to fit residues: 32.8047 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 520 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 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 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: 0.0060 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 = 0.5027 r_free = 0.5027 target = 0.221701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.204296 restraints weight = 13029.128| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 1.62 r_work: 0.4694 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7581 Z= 0.195 Angle : 0.739 11.937 10767 Z= 0.397 Chirality : 0.045 0.216 1177 Planarity : 0.007 0.065 999 Dihedral : 30.295 175.079 1953 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.59 % Favored : 88.44 % Rotamer: Outliers : 7.71 % Allowed : 18.88 % Favored : 73.41 % 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: -2.17 (0.34), residues: 623 helix: 0.38 (0.38), residues: 200 sheet: -2.59 (0.53), residues: 76 loop : -2.37 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 PHE 0.023 0.002 PHE D 562 TYR 0.013 0.003 TYR D 510 ARG 0.003 0.000 ARG C 496 Details of bonding type rmsd hydrogen bonds : bond 0.06144 ( 289) hydrogen bonds : angle 5.15064 ( 726) covalent geometry : bond 0.00458 ( 7581) covalent geometry : angle 0.73860 (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 128 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.5693 (mttt) cc_final: 0.5437 (mtmm) REVERT: A 602 ASP cc_start: 0.3336 (t0) cc_final: 0.2734 (p0) REVERT: B 475 ASN cc_start: 0.3708 (OUTLIER) cc_final: 0.3325 (t0) REVERT: B 556 GLU cc_start: 0.3655 (OUTLIER) cc_final: 0.3227 (pm20) REVERT: B 558 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6897 (pp) REVERT: C 543 MET cc_start: 0.2447 (ttm) cc_final: 0.2127 (tmm) REVERT: C 565 PHE cc_start: 0.5035 (m-10) cc_final: 0.4547 (m-80) REVERT: C 591 CYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4062 (p) REVERT: D 543 MET cc_start: 0.4228 (mtt) cc_final: 0.3856 (mtt) REVERT: D 584 MET cc_start: 0.6495 (tmt) cc_final: 0.6281 (tmt) outliers start: 40 outliers final: 24 residues processed: 119 average time/residue: 0.1926 time to fit residues: 30.7911 Evaluate side-chains 111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 591 CYS Chi-restraints excluded: chain D residue 502 THR 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 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 598 CYS 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: 0.2980 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 60 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.225437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.207868 restraints weight = 13126.060| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 1.70 r_work: 0.4737 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7581 Z= 0.163 Angle : 0.698 10.785 10767 Z= 0.377 Chirality : 0.043 0.246 1177 Planarity : 0.007 0.061 999 Dihedral : 30.052 177.208 1951 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.70 % Favored : 91.33 % Rotamer: Outliers : 5.39 % Allowed : 19.85 % 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: -2.00 (0.34), residues: 623 helix: 0.61 (0.38), residues: 204 sheet: -2.56 (0.54), residues: 75 loop : -2.35 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 609 HIS 0.004 0.001 HIS A 468 PHE 0.036 0.002 PHE D 610 TYR 0.013 0.002 TYR D 510 ARG 0.005 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.05476 ( 289) hydrogen bonds : angle 4.84151 ( 726) covalent geometry : bond 0.00378 ( 7581) covalent geometry : angle 0.69849 (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 118 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.2916 (t0) cc_final: 0.2453 (p0) REVERT: C 565 PHE cc_start: 0.4786 (m-10) cc_final: 0.4465 (m-80) outliers start: 28 outliers final: 21 residues processed: 111 average time/residue: 0.2111 time to fit residues: 31.3732 Evaluate side-chains 103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.6980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.5046 r_free = 0.5046 target = 0.223577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.206130 restraints weight = 13045.943| |-----------------------------------------------------------------------------| r_work (start): 0.4848 rms_B_bonded: 1.63 r_work: 0.4712 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7581 Z= 0.181 Angle : 0.718 10.860 10767 Z= 0.386 Chirality : 0.044 0.230 1177 Planarity : 0.007 0.063 999 Dihedral : 29.952 177.287 1951 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.59 % Favored : 88.44 % Rotamer: Outliers : 5.39 % Allowed : 21.58 % Favored : 73.03 % 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: 0.61 (0.39), residues: 203 sheet: -2.44 (0.55), residues: 73 loop : -2.41 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 609 HIS 0.005 0.001 HIS A 468 PHE 0.019 0.002 PHE D 562 TYR 0.019 0.003 TYR A 518 ARG 0.007 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 289) hydrogen bonds : angle 4.89242 ( 726) covalent geometry : bond 0.00423 ( 7581) covalent geometry : angle 0.71809 (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 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4186 (mt) REVERT: A 602 ASP cc_start: 0.3254 (t0) cc_final: 0.2604 (p0) REVERT: B 475 ASN cc_start: 0.3683 (OUTLIER) cc_final: 0.3264 (t0) REVERT: B 556 GLU cc_start: 0.3506 (OUTLIER) cc_final: 0.3195 (pm20) REVERT: C 565 PHE cc_start: 0.4858 (m-80) cc_final: 0.4461 (m-80) outliers start: 28 outliers final: 22 residues processed: 105 average time/residue: 0.2010 time to fit residues: 28.0236 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 598 CYS 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: 2.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.5050 r_free = 0.5050 target = 0.224118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.206649 restraints weight = 13186.466| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 1.64 r_work: 0.4715 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.5452 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= 0.175 Angle : 0.713 11.106 10767 Z= 0.383 Chirality : 0.043 0.246 1177 Planarity : 0.007 0.064 999 Dihedral : 29.857 178.341 1951 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.99 % Favored : 90.05 % Rotamer: Outliers : 5.59 % Allowed : 20.81 % 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: -2.06 (0.34), residues: 623 helix: 0.65 (0.38), residues: 203 sheet: -2.62 (0.52), residues: 78 loop : -2.43 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 609 HIS 0.002 0.001 HIS A 468 PHE 0.034 0.002 PHE D 610 TYR 0.014 0.002 TYR A 518 ARG 0.005 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.05506 ( 289) hydrogen bonds : angle 4.80027 ( 726) covalent geometry : bond 0.00411 ( 7581) covalent geometry : angle 0.71300 (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 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4241 (mt) REVERT: A 602 ASP cc_start: 0.3249 (t0) cc_final: 0.2594 (p0) REVERT: A 613 MET cc_start: 0.5677 (pmm) cc_final: 0.5468 (ttp) REVERT: B 475 ASN cc_start: 0.3557 (OUTLIER) cc_final: 0.3134 (t0) REVERT: C 565 PHE cc_start: 0.4819 (m-80) cc_final: 0.4481 (m-80) outliers start: 29 outliers final: 24 residues processed: 103 average time/residue: 0.1928 time to fit residues: 26.7424 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE 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 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 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 598 CYS 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: 1.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.5031 r_free = 0.5031 target = 0.221854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.204176 restraints weight = 13182.782| |-----------------------------------------------------------------------------| r_work (start): 0.4828 rms_B_bonded: 1.63 r_work: 0.4685 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.5639 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= 0.199 Angle : 0.746 11.711 10767 Z= 0.400 Chirality : 0.045 0.228 1177 Planarity : 0.007 0.064 999 Dihedral : 29.863 177.793 1951 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.27 % Favored : 88.76 % Rotamer: Outliers : 5.59 % Allowed : 20.81 % 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: -2.29 (0.34), residues: 623 helix: 0.65 (0.39), residues: 196 sheet: -2.75 (0.50), residues: 80 loop : -2.63 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 609 HIS 0.005 0.001 HIS A 468 PHE 0.020 0.002 PHE D 562 TYR 0.016 0.003 TYR A 518 ARG 0.004 0.000 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.05871 ( 289) hydrogen bonds : angle 4.96488 ( 726) covalent geometry : bond 0.00469 ( 7581) covalent geometry : angle 0.74637 (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 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4218 (mt) REVERT: A 602 ASP cc_start: 0.2988 (t0) cc_final: 0.2389 (p0) REVERT: A 613 MET cc_start: 0.5664 (pmm) cc_final: 0.5447 (ttp) REVERT: B 475 ASN cc_start: 0.3668 (OUTLIER) cc_final: 0.3249 (t0) REVERT: B 556 GLU cc_start: 0.3555 (OUTLIER) cc_final: 0.3191 (pm20) REVERT: C 565 PHE cc_start: 0.5084 (m-80) cc_final: 0.4574 (m-80) outliers start: 29 outliers final: 25 residues processed: 101 average time/residue: 0.2221 time to fit residues: 30.5531 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE 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 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 509 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 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 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** 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 = 0.5024 r_free = 0.5024 target = 0.220876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.203028 restraints weight = 13367.463| |-----------------------------------------------------------------------------| r_work (start): 0.4818 rms_B_bonded: 1.66 r_work: 0.4673 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7581 Z= 0.208 Angle : 0.761 11.036 10767 Z= 0.409 Chirality : 0.047 0.278 1177 Planarity : 0.008 0.065 999 Dihedral : 29.866 178.569 1951 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.41 % Rotamer: Outliers : 5.78 % Allowed : 20.23 % 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: -2.32 (0.34), residues: 623 helix: 0.49 (0.39), residues: 196 sheet: -2.58 (0.54), residues: 73 loop : -2.63 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 609 HIS 0.004 0.001 HIS A 468 PHE 0.022 0.002 PHE B 610 TYR 0.021 0.003 TYR A 518 ARG 0.003 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.05929 ( 289) hydrogen bonds : angle 5.12076 ( 726) covalent geometry : bond 0.00487 ( 7581) covalent geometry : angle 0.76100 (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 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4170 (mt) REVERT: A 602 ASP cc_start: 0.3019 (t0) cc_final: 0.2397 (p0) REVERT: B 475 ASN cc_start: 0.3629 (OUTLIER) cc_final: 0.3193 (t0) REVERT: B 556 GLU cc_start: 0.3868 (OUTLIER) cc_final: 0.3509 (pm20) REVERT: C 565 PHE cc_start: 0.5146 (m-80) cc_final: 0.4535 (m-80) outliers start: 30 outliers final: 26 residues processed: 102 average time/residue: 0.2454 time to fit residues: 34.2155 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE 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 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 B residue 567 GLN Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 509 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 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 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 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 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 = 0.5047 r_free = 0.5047 target = 0.223391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.206055 restraints weight = 13199.488| |-----------------------------------------------------------------------------| r_work (start): 0.4849 rms_B_bonded: 1.63 r_work: 0.4708 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.5970 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= 0.175 Angle : 0.721 10.931 10767 Z= 0.389 Chirality : 0.044 0.257 1177 Planarity : 0.007 0.065 999 Dihedral : 29.818 179.640 1951 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.41 % Rotamer: Outliers : 5.20 % Allowed : 21.00 % Favored : 73.80 % 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 (0.34), residues: 623 helix: 0.70 (0.39), residues: 197 sheet: -2.63 (0.50), residues: 82 loop : -2.57 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 503 HIS 0.005 0.001 HIS A 468 PHE 0.023 0.002 PHE B 565 TYR 0.023 0.002 TYR A 518 ARG 0.004 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 289) hydrogen bonds : angle 4.85940 ( 726) covalent geometry : bond 0.00410 ( 7581) covalent geometry : angle 0.72117 (10767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.55 seconds wall clock time: 75 minutes 42.22 seconds (4542.22 seconds total)