Starting phenix.real_space_refine on Mon Sep 23 23:59:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zyo_60574/09_2024/8zyo_60574.cif" } resolution = 3.29 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 4189 2.51 5 N 1003 2.21 5 O 1013 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6238 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1658 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1561 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain breaks: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1309 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 68 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 34 Unusual residues: {'XB7': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 34 Unusual residues: {'XB7': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AXB7 D1101 " occ=0.30 ... (66 atoms not shown) pdb=" O1 BXB7 D1101 " occ=0.70 Time building chain proxies: 5.03, per 1000 atoms: 0.81 Number of scatterers: 6238 At special positions: 0 Unit cell: (103.75, 115.37, 72.21, 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 31 16.00 F 2 9.00 O 1013 8.00 N 1003 7.00 C 4189 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: 1.61 Conformation dependent library (CDL) restraints added in 821.3 milliseconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 409 through 432 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 453 through 470 Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.705A pdb=" N TYR A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 4.154A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.722A pdb=" N SER A 543 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 575 Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 624 Processing helix chain 'A' and resid 634 through 656 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'B' and resid 408 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 453 through 471 removed outlier: 4.052A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.727A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.670A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.084A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 575 removed outlier: 3.697A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 663 removed outlier: 3.726A pdb=" N SER B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 432 removed outlier: 3.636A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 527 through 531 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 539 through 541 No H-bonds generated for 'chain 'C' and resid 539 through 541' Processing helix chain 'C' and resid 545 through 576 removed outlier: 3.647A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 594 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 665 removed outlier: 3.511A pdb=" N LEU C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 431 removed outlier: 4.338A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 453 through 470 Processing helix chain 'D' and resid 489 through 494 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 521 through 526 Processing helix chain 'D' and resid 527 through 530 Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.958A pdb=" N VAL D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.546A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 575 removed outlier: 3.697A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 665 removed outlier: 4.207A pdb=" N GLN D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 665 " --> pdb=" O ALA D 661 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1829 1.34 - 1.46: 1628 1.46 - 1.58: 2882 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 6389 Sorted by residual: bond pdb=" C20BXB7 D1101 " pdb=" C21BXB7 D1101 " ideal model delta sigma weight residual 1.511 1.386 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C5 BXB7 D1101 " pdb=" C6 BXB7 D1101 " ideal model delta sigma weight residual 1.503 1.380 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C20AXB7 D1101 " pdb=" C21AXB7 D1101 " ideal model delta sigma weight residual 1.511 1.389 0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C5 AXB7 D1101 " pdb=" C6 AXB7 D1101 " ideal model delta sigma weight residual 1.503 1.381 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C14AXB7 D1101 " pdb=" C19AXB7 D1101 " ideal model delta sigma weight residual 1.406 1.332 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 6384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8486 2.04 - 4.08: 137 4.08 - 6.12: 37 6.12 - 8.16: 7 8.16 - 10.20: 3 Bond angle restraints: 8670 Sorted by residual: angle pdb=" CB LYS D 434 " pdb=" CG LYS D 434 " pdb=" CD LYS D 434 " ideal model delta sigma weight residual 111.30 121.50 -10.20 2.30e+00 1.89e-01 1.97e+01 angle pdb=" N ASN D 629 " pdb=" CA ASN D 629 " pdb=" C ASN D 629 " ideal model delta sigma weight residual 110.97 106.46 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" CA PHE D 627 " pdb=" C PHE D 627 " pdb=" O PHE D 627 " ideal model delta sigma weight residual 120.20 115.66 4.54 1.12e+00 7.97e-01 1.64e+01 angle pdb=" C LEU D 524 " pdb=" N LYS D 525 " pdb=" CA LYS D 525 " ideal model delta sigma weight residual 121.94 114.50 7.44 2.00e+00 2.50e-01 1.38e+01 angle pdb=" N PHE A 627 " pdb=" CA PHE A 627 " pdb=" CB PHE A 627 " ideal model delta sigma weight residual 110.28 104.58 5.70 1.55e+00 4.16e-01 1.35e+01 ... (remaining 8665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.65: 3370 25.65 - 51.30: 268 51.30 - 76.95: 15 76.95 - 102.60: 2 102.60 - 128.25: 2 Dihedral angle restraints: 3657 sinusoidal: 1391 harmonic: 2266 Sorted by residual: dihedral pdb=" C10BXB7 D1101 " pdb=" C8 BXB7 D1101 " pdb=" C9 BXB7 D1101 " pdb=" N1 BXB7 D1101 " ideal model delta sinusoidal sigma weight residual -56.72 71.53 -128.25 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" CA PHE B 656 " pdb=" C PHE B 656 " pdb=" N GLY B 657 " pdb=" CA GLY B 657 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C12BXB7 D1101 " pdb=" C8 BXB7 D1101 " pdb=" N1 BXB7 D1101 " pdb=" C9 BXB7 D1101 " ideal model delta sinusoidal sigma weight residual 59.79 -45.51 105.30 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 797 0.046 - 0.093: 196 0.093 - 0.139: 21 0.139 - 0.185: 6 0.185 - 0.231: 2 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA VAL D 630 " pdb=" N VAL D 630 " pdb=" C VAL D 630 " pdb=" CB VAL D 630 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 656 " pdb=" N PHE C 656 " pdb=" C PHE C 656 " pdb=" CB PHE C 656 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA PHE D 627 " pdb=" N PHE D 627 " pdb=" C PHE D 627 " pdb=" CB PHE D 627 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 1019 not shown) Planarity restraints: 1017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 649 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C SER D 649 " -0.030 2.00e-02 2.50e+03 pdb=" O SER D 649 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 650 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 625 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C VAL D 625 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 625 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 626 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 506 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 507 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " -0.022 5.00e-02 4.00e+02 ... (remaining 1014 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1169 2.76 - 3.30: 6120 3.30 - 3.83: 10587 3.83 - 4.37: 11494 4.37 - 4.90: 20166 Nonbonded interactions: 49536 Sorted by model distance: nonbonded pdb=" O LEU B 539 " pdb=" OG SER B 543 " model vdw 2.227 3.040 nonbonded pdb=" O LEU C 523 " pdb=" OG1 THR C 526 " model vdw 2.232 3.040 nonbonded pdb=" O PHE D 619 " pdb=" OG1 THR D 623 " model vdw 2.236 3.040 nonbonded pdb=" O PRO A 632 " pdb=" ND2 ASN B 629 " model vdw 2.256 3.120 nonbonded pdb=" O SER D 624 " pdb=" OG SER D 624 " model vdw 2.269 3.040 ... (remaining 49531 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 407 through 471 or (resid 498 and (name N or name CA or na \ me C or name O or name CB )) or resid 499 through 665)) selection = chain 'B' selection = (chain 'D' and (resid 407 through 471 or (resid 498 and (name N or name CA or na \ me C or name O or name CB )) or resid 499 through 665)) } 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=0.30 max=1.00 mean=0.99 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.200 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.005 0.125 6389 Z= 0.320 Angle : 0.675 10.197 8670 Z= 0.354 Chirality : 0.040 0.231 1022 Planarity : 0.004 0.039 1017 Dihedral : 17.016 128.249 2191 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.46 % Allowed : 31.11 % Favored : 68.42 % 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: 1.70 (0.31), residues: 741 helix: 1.47 (0.22), residues: 580 sheet: None (None), residues: 0 loop : 0.09 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 585 HIS 0.005 0.001 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.016 0.002 TYR A 616 ARG 0.004 0.000 ARG D 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 ARG cc_start: 0.8393 (ptm160) cc_final: 0.8071 (ptt180) REVERT: A 574 MET cc_start: 0.8365 (mmm) cc_final: 0.8071 (mmm) REVERT: A 616 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8473 (t80) REVERT: C 608 LYS cc_start: 0.9083 (tttt) cc_final: 0.8684 (tttp) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.2270 time to fit residues: 35.9529 Evaluate side-chains 123 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6389 Z= 0.175 Angle : 0.515 6.530 8670 Z= 0.269 Chirality : 0.037 0.145 1022 Planarity : 0.003 0.035 1017 Dihedral : 8.161 102.808 864 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.64 % Allowed : 25.54 % Favored : 69.81 % 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: 1.91 (0.32), residues: 741 helix: 1.49 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.66 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.004 0.001 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.017 0.002 TYR A 616 ARG 0.003 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 ARG cc_start: 0.8362 (ptm160) cc_final: 0.8102 (ptt180) REVERT: A 616 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8386 (t80) REVERT: C 528 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7929 (mtt180) outliers start: 30 outliers final: 16 residues processed: 141 average time/residue: 0.2113 time to fit residues: 37.6728 Evaluate side-chains 134 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 69 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6389 Z= 0.191 Angle : 0.515 6.234 8670 Z= 0.267 Chirality : 0.037 0.144 1022 Planarity : 0.003 0.031 1017 Dihedral : 8.069 99.953 864 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.42 % Allowed : 25.54 % Favored : 69.04 % 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: 1.93 (0.32), residues: 741 helix: 1.47 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.86 (0.58), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.003 0.001 HIS A 492 PHE 0.014 0.001 PHE D 656 TYR 0.018 0.002 TYR A 616 ARG 0.003 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8423 (mmm) cc_final: 0.8034 (mmm) REVERT: B 554 MET cc_start: 0.8571 (tpp) cc_final: 0.8261 (mmp) REVERT: C 528 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7953 (mtt180) REVERT: C 597 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8377 (m-80) outliers start: 35 outliers final: 26 residues processed: 138 average time/residue: 0.2008 time to fit residues: 35.1893 Evaluate side-chains 143 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 526 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6389 Z= 0.167 Angle : 0.494 6.241 8670 Z= 0.256 Chirality : 0.037 0.143 1022 Planarity : 0.003 0.031 1017 Dihedral : 7.810 96.496 862 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.80 % Allowed : 25.54 % Favored : 69.66 % 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 (0.32), residues: 741 helix: 1.53 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.89 (0.58), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.003 0.000 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.016 0.002 TYR A 616 ARG 0.002 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8392 (t80) REVERT: A 656 PHE cc_start: 0.8247 (m-80) cc_final: 0.8030 (m-80) REVERT: B 554 MET cc_start: 0.8601 (tpp) cc_final: 0.8311 (mmp) REVERT: B 557 PHE cc_start: 0.8783 (t80) cc_final: 0.8567 (t80) REVERT: C 528 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7976 (mtt180) REVERT: C 597 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: D 597 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7873 (t80) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 0.2129 time to fit residues: 36.9257 Evaluate side-chains 140 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 526 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6389 Z= 0.194 Angle : 0.523 7.598 8670 Z= 0.268 Chirality : 0.037 0.144 1022 Planarity : 0.003 0.031 1017 Dihedral : 7.539 88.480 862 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.26 % Allowed : 25.08 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.32), residues: 741 helix: 1.49 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.93 (0.59), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.003 0.000 HIS A 492 PHE 0.014 0.001 PHE D 656 TYR 0.017 0.002 TYR A 616 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.8488 (mmm) cc_final: 0.8163 (mmm) REVERT: A 656 PHE cc_start: 0.8268 (m-80) cc_final: 0.8047 (m-80) REVERT: B 539 LEU cc_start: 0.8882 (tt) cc_final: 0.8573 (tp) REVERT: B 554 MET cc_start: 0.8612 (tpp) cc_final: 0.8344 (mmp) REVERT: B 557 PHE cc_start: 0.8786 (t80) cc_final: 0.8572 (t80) REVERT: C 528 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7932 (mtt180) REVERT: C 597 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: D 462 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: D 597 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7935 (t80) outliers start: 34 outliers final: 24 residues processed: 141 average time/residue: 0.2225 time to fit residues: 39.5112 Evaluate side-chains 142 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 526 THR Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0050 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6389 Z= 0.166 Angle : 0.493 6.920 8670 Z= 0.255 Chirality : 0.037 0.143 1022 Planarity : 0.003 0.029 1017 Dihedral : 5.857 88.262 862 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.64 % Allowed : 25.54 % Favored : 69.81 % 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: 2.09 (0.32), residues: 741 helix: 1.56 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 1.00 (0.59), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.003 0.000 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.015 0.001 TYR D 616 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.4956 (p90) REVERT: A 574 MET cc_start: 0.8458 (mmm) cc_final: 0.8104 (mmm) REVERT: A 616 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8395 (t80) REVERT: A 656 PHE cc_start: 0.8158 (m-80) cc_final: 0.7939 (m-80) REVERT: B 457 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5416 (mt) REVERT: B 539 LEU cc_start: 0.8835 (tt) cc_final: 0.8549 (tp) REVERT: B 557 PHE cc_start: 0.8767 (t80) cc_final: 0.8547 (t80) REVERT: B 651 MET cc_start: 0.7504 (mmt) cc_final: 0.7150 (mmt) REVERT: C 528 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7921 (mtt180) REVERT: C 597 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: D 462 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7566 (mmm) REVERT: D 597 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7899 (t80) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 0.2038 time to fit residues: 36.1357 Evaluate side-chains 140 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 493 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6389 Z= 0.214 Angle : 0.528 6.191 8670 Z= 0.276 Chirality : 0.038 0.145 1022 Planarity : 0.003 0.029 1017 Dihedral : 5.948 86.237 862 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.57 % Allowed : 25.85 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.32), residues: 741 helix: 1.49 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.90 (0.58), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.002 0.000 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.018 0.002 TYR A 616 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.4912 (p90) REVERT: A 616 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 457 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5458 (mt) REVERT: B 539 LEU cc_start: 0.8817 (tt) cc_final: 0.8528 (tp) REVERT: B 557 PHE cc_start: 0.8794 (t80) cc_final: 0.8568 (t80) REVERT: C 597 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: C 651 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5482 (mtt) REVERT: D 597 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7950 (t80) outliers start: 36 outliers final: 25 residues processed: 139 average time/residue: 0.2047 time to fit residues: 36.0399 Evaluate side-chains 146 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 493 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 526 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6389 Z= 0.174 Angle : 0.505 6.056 8670 Z= 0.263 Chirality : 0.037 0.143 1022 Planarity : 0.003 0.030 1017 Dihedral : 5.875 89.120 862 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.49 % Allowed : 26.63 % Favored : 68.89 % 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: 2.09 (0.32), residues: 741 helix: 1.57 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.96 (0.58), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.003 0.000 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.016 0.001 TYR A 616 ARG 0.003 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.4912 (p90) REVERT: A 574 MET cc_start: 0.8489 (mmm) cc_final: 0.8251 (mmm) REVERT: A 616 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 457 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5483 (mt) REVERT: B 539 LEU cc_start: 0.8798 (tt) cc_final: 0.8502 (tp) REVERT: C 597 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: D 597 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7964 (t80) outliers start: 29 outliers final: 22 residues processed: 139 average time/residue: 0.1994 time to fit residues: 35.3466 Evaluate side-chains 144 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 493 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 526 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6389 Z= 0.183 Angle : 0.514 5.962 8670 Z= 0.269 Chirality : 0.038 0.143 1022 Planarity : 0.003 0.030 1017 Dihedral : 5.887 87.344 862 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.33 % Allowed : 26.78 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.32), residues: 741 helix: 1.58 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 1.00 (0.59), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.003 0.000 HIS A 492 PHE 0.014 0.001 PHE A 557 TYR 0.017 0.002 TYR A 616 ARG 0.003 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7478 (mtmm) REVERT: A 493 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.4899 (p90) REVERT: A 574 MET cc_start: 0.8527 (mmm) cc_final: 0.8244 (mmm) REVERT: A 616 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8471 (t80) REVERT: B 457 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5555 (mt) REVERT: B 539 LEU cc_start: 0.8756 (tt) cc_final: 0.8403 (tp) REVERT: C 597 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: D 597 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7940 (t80) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 0.2122 time to fit residues: 37.2715 Evaluate side-chains 144 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 493 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6389 Z= 0.147 Angle : 0.502 7.212 8670 Z= 0.260 Chirality : 0.037 0.147 1022 Planarity : 0.003 0.030 1017 Dihedral : 5.783 89.430 862 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.33 % Allowed : 26.63 % Favored : 69.04 % 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: 2.30 (0.32), residues: 741 helix: 1.72 (0.22), residues: 588 sheet: None (None), residues: 0 loop : 1.03 (0.58), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.003 0.000 HIS A 492 PHE 0.016 0.001 PHE A 557 TYR 0.014 0.001 TYR A 616 ARG 0.003 0.000 ARG A 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7400 (mtmm) REVERT: A 493 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.4795 (p90) REVERT: A 574 MET cc_start: 0.8499 (mmm) cc_final: 0.8259 (mmm) REVERT: A 616 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 457 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5564 (mt) REVERT: C 597 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 597 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7972 (t80) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 0.2132 time to fit residues: 38.9700 Evaluate side-chains 141 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 493 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 616 TYR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 606 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125367 restraints weight = 9953.963| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.19 r_work: 0.3233 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6389 Z= 0.268 Angle : 0.569 6.209 8670 Z= 0.298 Chirality : 0.040 0.157 1022 Planarity : 0.004 0.030 1017 Dihedral : 5.944 85.816 862 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.02 % Allowed : 27.55 % Favored : 68.42 % 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: 1.94 (0.32), residues: 741 helix: 1.46 (0.22), residues: 590 sheet: None (None), residues: 0 loop : 0.91 (0.59), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.002 0.001 HIS A 492 PHE 0.013 0.001 PHE D 656 TYR 0.021 0.002 TYR A 616 ARG 0.003 0.000 ARG A 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.18 seconds wall clock time: 35 minutes 29.06 seconds (2129.06 seconds total)