Starting phenix.real_space_refine on Thu Feb 15 07:25:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_27500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_27500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_27500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_27500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlf_27500/02_2024/8dlf_27500.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.64, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 3.81 Conformation dependent library (CDL) restraints added in 971.1 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: 3.29 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: 2.05 Time building geometry restraints manager: 4.07 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: 96.31 - 103.90: 391 103.90 - 111.49: 3715 111.49 - 119.08: 2969 119.08 - 126.67: 3301 126.67 - 134.26: 391 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 2.520 nonbonded pdb=" NH1 ARG C 538 " pdb=" O SER C 557 " model vdw 2.243 2.520 nonbonded pdb=" OG SER C 599 " pdb=" O SER D 599 " model vdw 2.255 2.440 nonbonded pdb=" O PRO C 476 " pdb=" ND2 ASN C 480 " model vdw 2.267 2.520 nonbonded pdb=" O LEU D 582 " pdb=" OG1 THR D 585 " model vdw 2.277 2.440 ... (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 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: 0.760 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: 0.010 Extract box with map and model: 3.130 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.810 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- 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= 0.448 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 *********************** 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 fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 0.744 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: 0.2317 time to fit residues: 52.2698 Evaluate side-chains 113 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 55 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4666 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7581 Z= 0.254 Angle : 0.772 12.828 10767 Z= 0.420 Chirality : 0.046 0.211 1177 Planarity : 0.007 0.057 999 Dihedral : 30.341 179.323 1975 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.67 % Favored : 90.21 % Rotamer: Outliers : 6.74 % Allowed : 15.22 % Favored : 78.03 % 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: -1.74 (0.34), residues: 623 helix: 0.96 (0.38), residues: 196 sheet: -2.04 (0.54), residues: 81 loop : -2.30 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 503 HIS 0.003 0.001 HIS A 468 PHE 0.026 0.002 PHE D 610 TYR 0.009 0.002 TYR B 518 ARG 0.003 0.000 ARG C 522 *********************** 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 143 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.3858 (OUTLIER) cc_final: 0.3295 (m170) REVERT: A 602 ASP cc_start: 0.2874 (t0) cc_final: 0.1967 (p0) REVERT: B 497 THR cc_start: 0.6000 (OUTLIER) cc_final: 0.5574 (t) REVERT: B 556 GLU cc_start: 0.3231 (OUTLIER) cc_final: 0.2495 (pm20) REVERT: B 558 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6952 (pp) REVERT: C 497 THR cc_start: 0.6373 (OUTLIER) cc_final: 0.5827 (t) REVERT: C 563 MET cc_start: 0.6299 (ttm) cc_final: 0.6089 (ttm) REVERT: C 565 PHE cc_start: 0.4868 (m-10) cc_final: 0.4372 (m-80) REVERT: D 510 TYR cc_start: 0.6980 (p90) cc_final: 0.6563 (p90) outliers start: 35 outliers final: 15 residues processed: 136 average time/residue: 0.2014 time to fit residues: 36.2445 Evaluate side-chains 111 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 B residue 468 HIS Chi-restraints excluded: chain B residue 497 THR 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 558 ILE Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 517 LEU 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 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5038 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7581 Z= 0.429 Angle : 0.904 14.219 10767 Z= 0.483 Chirality : 0.054 0.256 1177 Planarity : 0.008 0.061 999 Dihedral : 30.361 174.791 1961 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 36.61 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.75 % Favored : 88.12 % Rotamer: Outliers : 8.48 % Allowed : 17.73 % 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: -2.39 (0.33), residues: 623 helix: 0.09 (0.37), residues: 195 sheet: -2.21 (0.57), residues: 73 loop : -2.54 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 609 HIS 0.004 0.001 HIS C 569 PHE 0.021 0.003 PHE D 562 TYR 0.022 0.004 TYR C 510 ARG 0.010 0.001 ARG A 469 *********************** 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 137 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 93 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4730 (OUTLIER) cc_final: 0.4365 (m170) REVERT: A 602 ASP cc_start: 0.2318 (t0) cc_final: 0.1894 (p0) REVERT: B 556 GLU cc_start: 0.4196 (OUTLIER) cc_final: 0.3660 (pm20) REVERT: B 558 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6955 (pp) REVERT: C 497 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.5936 (t) REVERT: C 565 PHE cc_start: 0.5423 (m-10) cc_final: 0.4298 (m-80) REVERT: D 517 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6427 (mt) REVERT: D 565 PHE cc_start: 0.2573 (OUTLIER) cc_final: 0.1172 (m-80) outliers start: 44 outliers final: 26 residues processed: 126 average time/residue: 0.2069 time to fit residues: 34.3371 Evaluate side-chains 114 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS 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 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 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 543 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 481 ILE 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 534 THR 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 592 ASN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4909 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7581 Z= 0.271 Angle : 0.759 12.437 10767 Z= 0.410 Chirality : 0.046 0.199 1177 Planarity : 0.007 0.059 999 Dihedral : 30.397 173.757 1960 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 30.31 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.47 % Favored : 89.41 % Rotamer: Outliers : 6.94 % Allowed : 20.62 % Favored : 72.45 % 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: -2.33 (0.34), residues: 623 helix: 0.39 (0.38), residues: 198 sheet: -2.77 (0.51), residues: 85 loop : -2.50 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 PHE 0.034 0.003 PHE D 610 TYR 0.011 0.002 TYR B 518 ARG 0.005 0.000 ARG D 538 *********************** 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 131 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4700 (OUTLIER) cc_final: 0.4151 (m170) REVERT: A 602 ASP cc_start: 0.2547 (t0) cc_final: 0.1999 (p0) REVERT: B 461 LYS cc_start: 0.2190 (mmmt) cc_final: 0.1578 (mtmt) REVERT: B 556 GLU cc_start: 0.3587 (OUTLIER) cc_final: 0.3125 (pm20) REVERT: B 558 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6912 (pp) REVERT: C 497 THR cc_start: 0.6474 (OUTLIER) cc_final: 0.5928 (t) REVERT: C 543 MET cc_start: 0.1794 (OUTLIER) cc_final: 0.1182 (tmm) REVERT: C 565 PHE cc_start: 0.5048 (m-80) cc_final: 0.4308 (m-80) REVERT: D 510 TYR cc_start: 0.7151 (p90) cc_final: 0.6560 (p90) REVERT: D 565 PHE cc_start: 0.2284 (OUTLIER) cc_final: 0.1452 (m-80) outliers start: 36 outliers final: 21 residues processed: 123 average time/residue: 0.2066 time to fit residues: 33.6469 Evaluate side-chains 112 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 499 ASP Chi-restraints excluded: chain A residue 516 SER 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 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 497 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7581 Z= 0.359 Angle : 0.838 14.243 10767 Z= 0.449 Chirality : 0.050 0.244 1177 Planarity : 0.008 0.063 999 Dihedral : 30.451 174.934 1954 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 34.51 Ramachandran Plot: Outliers : 1.12 % Allowed : 11.40 % Favored : 87.48 % Rotamer: Outliers : 8.48 % Allowed : 20.42 % Favored : 71.10 % 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: -2.60 (0.33), residues: 623 helix: 0.04 (0.38), residues: 200 sheet: -2.87 (0.51), residues: 77 loop : -2.63 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 503 HIS 0.003 0.001 HIS C 569 PHE 0.026 0.003 PHE D 562 TYR 0.018 0.004 TYR C 510 ARG 0.004 0.001 ARG A 538 *********************** 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 127 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 83 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.2604 (t0) cc_final: 0.2111 (p0) REVERT: B 556 GLU cc_start: 0.3822 (OUTLIER) cc_final: 0.3348 (pm20) REVERT: B 558 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6926 (pp) REVERT: C 543 MET cc_start: 0.2291 (ttm) cc_final: 0.1976 (tmm) REVERT: C 565 PHE cc_start: 0.5154 (m-80) cc_final: 0.4256 (m-80) REVERT: D 510 TYR cc_start: 0.7218 (p90) cc_final: 0.6652 (p90) REVERT: D 565 PHE cc_start: 0.2550 (OUTLIER) cc_final: 0.1878 (m-80) REVERT: D 584 MET cc_start: 0.6184 (tmt) cc_final: 0.5921 (tmt) outliers start: 44 outliers final: 28 residues processed: 118 average time/residue: 0.1792 time to fit residues: 28.5931 Evaluate side-chains 111 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 499 ASP Chi-restraints excluded: chain A residue 516 SER 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 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 499 ASP 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 502 THR 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 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 598 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** A 480 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7581 Z= 0.245 Angle : 0.736 11.832 10767 Z= 0.398 Chirality : 0.045 0.237 1177 Planarity : 0.007 0.063 999 Dihedral : 30.317 178.051 1951 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.15 % Favored : 89.89 % Rotamer: Outliers : 6.36 % Allowed : 22.54 % Favored : 71.10 % 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: -2.34 (0.34), residues: 623 helix: 0.55 (0.38), residues: 196 sheet: -2.81 (0.51), residues: 82 loop : -2.61 (0.33), residues: 345 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 0.021 0.002 PHE D 562 TYR 0.009 0.002 TYR B 561 ARG 0.003 0.000 ARG A 532 *********************** 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 123 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4869 (OUTLIER) cc_final: 0.4550 (m-70) REVERT: A 602 ASP cc_start: 0.2620 (t0) cc_final: 0.1803 (p0) REVERT: B 558 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6983 (pp) REVERT: C 563 MET cc_start: 0.6210 (ttm) cc_final: 0.5978 (ttm) REVERT: C 565 PHE cc_start: 0.4823 (m-80) cc_final: 0.4284 (m-80) REVERT: D 510 TYR cc_start: 0.7189 (p90) cc_final: 0.6919 (p90) REVERT: D 584 MET cc_start: 0.6321 (tmt) cc_final: 0.6013 (tmt) outliers start: 33 outliers final: 28 residues processed: 115 average time/residue: 0.1923 time to fit residues: 30.4850 Evaluate side-chains 116 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 499 ASP Chi-restraints excluded: chain A residue 503 TRP Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER 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 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 503 TRP 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 598 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7581 Z= 0.338 Angle : 0.801 12.787 10767 Z= 0.429 Chirality : 0.049 0.235 1177 Planarity : 0.008 0.065 999 Dihedral : 30.187 176.959 1951 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 1.12 % Allowed : 12.04 % Favored : 86.84 % Rotamer: Outliers : 6.55 % Allowed : 23.31 % Favored : 70.13 % 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: -2.52 (0.33), residues: 623 helix: 0.36 (0.39), residues: 188 sheet: -2.63 (0.52), residues: 73 loop : -2.73 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 609 HIS 0.013 0.001 HIS A 468 PHE 0.023 0.003 PHE D 562 TYR 0.019 0.003 TYR A 518 ARG 0.004 0.000 ARG A 538 *********************** 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 116 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.2737 (t0) cc_final: 0.2076 (p0) REVERT: B 556 GLU cc_start: 0.3618 (OUTLIER) cc_final: 0.3110 (pm20) REVERT: B 558 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7032 (pp) REVERT: C 565 PHE cc_start: 0.5065 (m-80) cc_final: 0.4226 (m-80) REVERT: D 510 TYR cc_start: 0.6991 (p90) cc_final: 0.6435 (p90) REVERT: D 565 PHE cc_start: 0.2358 (OUTLIER) cc_final: 0.1816 (m-80) REVERT: D 584 MET cc_start: 0.6332 (tmt) cc_final: 0.6033 (tmt) outliers start: 34 outliers final: 28 residues processed: 107 average time/residue: 0.1903 time to fit residues: 27.5397 Evaluate side-chains 112 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 503 TRP Chi-restraints excluded: chain A residue 516 SER 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 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 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 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 592 ASN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 598 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** A 480 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4874 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7581 Z= 0.237 Angle : 0.723 10.588 10767 Z= 0.389 Chirality : 0.045 0.243 1177 Planarity : 0.007 0.064 999 Dihedral : 30.034 178.624 1951 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.99 % Favored : 90.05 % Rotamer: Outliers : 5.97 % Allowed : 23.51 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.33), residues: 623 helix: 0.60 (0.38), residues: 196 sheet: -2.79 (0.51), residues: 82 loop : -2.71 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 464 HIS 0.007 0.001 HIS A 468 PHE 0.036 0.002 PHE D 610 TYR 0.010 0.002 TYR C 561 ARG 0.003 0.000 ARG D 532 *********************** 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 121 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.3972 (OUTLIER) cc_final: 0.3744 (mt) REVERT: A 563 MET cc_start: 0.5968 (tpt) cc_final: 0.5700 (tpt) REVERT: A 602 ASP cc_start: 0.2759 (t0) cc_final: 0.1864 (p0) REVERT: B 558 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7038 (pp) REVERT: C 565 PHE cc_start: 0.4861 (m-80) cc_final: 0.4262 (m-80) outliers start: 31 outliers final: 28 residues processed: 113 average time/residue: 0.2032 time to fit residues: 30.8452 Evaluate side-chains 116 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 499 ASP Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER 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 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 503 TRP 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 592 ASN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 598 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7581 Z= 0.299 Angle : 0.772 12.088 10767 Z= 0.413 Chirality : 0.047 0.246 1177 Planarity : 0.008 0.065 999 Dihedral : 29.948 178.041 1951 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.56 % Favored : 87.48 % Rotamer: Outliers : 6.94 % Allowed : 21.77 % Favored : 71.29 % 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: -2.42 (0.33), residues: 623 helix: 0.45 (0.38), residues: 197 sheet: -2.58 (0.52), residues: 75 loop : -2.74 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 609 HIS 0.002 0.001 HIS C 468 PHE 0.022 0.002 PHE B 610 TYR 0.015 0.003 TYR A 518 ARG 0.006 0.000 ARG C 469 *********************** 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 120 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5822 (m-30) REVERT: A 526 LEU cc_start: 0.3900 (OUTLIER) cc_final: 0.3690 (mt) REVERT: A 584 MET cc_start: 0.5071 (mmt) cc_final: 0.4069 (tpt) REVERT: A 602 ASP cc_start: 0.2677 (t0) cc_final: 0.1819 (p0) REVERT: B 556 GLU cc_start: 0.3440 (OUTLIER) cc_final: 0.2897 (pm20) REVERT: B 558 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.7013 (pp) REVERT: C 565 PHE cc_start: 0.4934 (m-80) cc_final: 0.4226 (m-80) REVERT: D 510 TYR cc_start: 0.7037 (p90) cc_final: 0.6555 (p90) outliers start: 36 outliers final: 28 residues processed: 109 average time/residue: 0.1992 time to fit residues: 29.0444 Evaluate side-chains 113 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 521 ARG 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 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 D residue 503 TRP 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 598 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4866 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7581 Z= 0.242 Angle : 0.727 10.694 10767 Z= 0.391 Chirality : 0.045 0.262 1177 Planarity : 0.007 0.064 999 Dihedral : 29.851 179.382 1951 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.31 % Favored : 89.73 % Rotamer: Outliers : 5.39 % Allowed : 23.31 % Favored : 71.29 % 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: -2.33 (0.33), residues: 623 helix: 0.62 (0.38), residues: 198 sheet: -2.65 (0.51), residues: 82 loop : -2.71 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 503 HIS 0.001 0.000 HIS A 468 PHE 0.029 0.002 PHE D 610 TYR 0.017 0.002 TYR B 510 ARG 0.005 0.000 ARG C 469 ********************** 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 112 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 MET cc_start: 0.4852 (mmt) cc_final: 0.4120 (tpt) REVERT: A 602 ASP cc_start: 0.2837 (t0) cc_final: 0.1932 (p0) REVERT: C 565 PHE cc_start: 0.4810 (m-80) cc_final: 0.4228 (m-80) outliers start: 28 outliers final: 25 residues processed: 104 average time/residue: 0.1958 time to fit residues: 27.3929 Evaluate side-chains 108 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 524 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 503 TRP 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 577 ASP 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 600 PHE 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 57 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 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 = 0.5043 r_free = 0.5043 target = 0.223183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.206012 restraints weight = 12977.965| |-----------------------------------------------------------------------------| r_work (start): 0.4850 rms_B_bonded: 1.60 r_work: 0.4711 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7581 Z= 0.233 Angle : 0.716 10.239 10767 Z= 0.385 Chirality : 0.045 0.313 1177 Planarity : 0.007 0.065 999 Dihedral : 29.783 179.722 1949 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.41 % Rotamer: Outliers : 5.20 % Allowed : 23.12 % Favored : 71.68 % 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: -2.21 (0.34), residues: 623 helix: 0.71 (0.38), residues: 198 sheet: -2.45 (0.53), residues: 82 loop : -2.67 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 609 HIS 0.003 0.000 HIS C 468 PHE 0.022 0.002 PHE B 610 TYR 0.014 0.002 TYR B 510 ARG 0.003 0.000 ARG C 469 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.70 seconds wall clock time: 32 minutes 19.24 seconds (1939.24 seconds total)