Starting phenix.real_space_refine on Thu Jun 5 18:30:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.map" model { file = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wxh_32879/06_2025/7wxh_32879.cif" } resolution = 4.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4054 2.51 5 N 1172 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6494 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3247 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 414} Restraints were copied for chains: B Time building chain proxies: 5.47, per 1000 atoms: 0.84 Number of scatterers: 6494 At special positions: 0 Unit cell: (98.58, 94.34, 62.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1238 8.00 N 1172 7.00 C 4054 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: 1.53 Conformation dependent library (CDL) restraints added in 885.4 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 47.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.266A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.126A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.629A pdb=" N THR A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.792A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.586A pdb=" N ALA A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 4.266A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.127A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.629A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.792A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.586A pdb=" N ALA B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 744 through 750 removed outlier: 7.301A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A 456 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 440 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 445 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 771 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.479A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS A 490 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 464 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 removed outlier: 7.447A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.625A pdb=" N LYS A 629 " --> pdb=" O CYS A 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.272A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 744 through 750 removed outlier: 7.300A pdb=" N LEU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR B 456 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 440 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 445 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 771 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 487 through 490 removed outlier: 6.478A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LYS B 490 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 464 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.447A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 629 through 630 removed outlier: 6.625A pdb=" N LYS B 629 " --> pdb=" O CYS B 659 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.273A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 840 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: 3.63 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.46: 1115 1.46 - 1.57: 3173 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6594 Sorted by residual: bond pdb=" C LYS B 629 " pdb=" N ILE B 630 " ideal model delta sigma weight residual 1.330 1.311 0.020 1.42e-02 4.96e+03 1.91e+00 bond pdb=" C ARG A 411 " pdb=" N LEU A 412 " ideal model delta sigma weight residual 1.334 1.316 0.019 1.38e-02 5.25e+03 1.85e+00 bond pdb=" CG LEU B 389 " pdb=" CD1 LEU B 389 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CG LEU A 389 " pdb=" CD1 LEU A 389 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CA GLY A 764 " pdb=" C GLY A 764 " ideal model delta sigma weight residual 1.519 1.509 0.009 7.00e-03 2.04e+04 1.78e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 8875 3.61 - 7.22: 49 7.22 - 10.84: 2 10.84 - 14.45: 0 14.45 - 18.06: 2 Bond angle restraints: 8928 Sorted by residual: angle pdb=" CA LEU A 389 " pdb=" CB LEU A 389 " pdb=" CG LEU A 389 " ideal model delta sigma weight residual 116.30 134.36 -18.06 3.50e+00 8.16e-02 2.66e+01 angle pdb=" CA LEU B 389 " pdb=" CB LEU B 389 " pdb=" CG LEU B 389 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" C LEU B 389 " pdb=" N ASP B 390 " pdb=" CA ASP B 390 " ideal model delta sigma weight residual 120.29 115.40 4.89 1.42e+00 4.96e-01 1.19e+01 angle pdb=" C LEU A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta sigma weight residual 120.29 115.43 4.86 1.42e+00 4.96e-01 1.17e+01 angle pdb=" CA GLU A 526 " pdb=" CB GLU A 526 " pdb=" CG GLU A 526 " ideal model delta sigma weight residual 114.10 107.76 6.34 2.00e+00 2.50e-01 1.00e+01 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 3517 14.78 - 29.57: 376 29.57 - 44.35: 111 44.35 - 59.13: 28 59.13 - 73.92: 4 Dihedral angle restraints: 4036 sinusoidal: 1572 harmonic: 2464 Sorted by residual: dihedral pdb=" CA GLN B 638 " pdb=" C GLN B 638 " pdb=" N GLN B 639 " pdb=" CA GLN B 639 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLN A 638 " pdb=" C GLN A 638 " pdb=" N GLN A 639 " pdb=" CA GLN A 639 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA THR A 524 " pdb=" C THR A 524 " pdb=" N ARG A 525 " pdb=" CA ARG A 525 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 564 0.028 - 0.057: 286 0.057 - 0.085: 136 0.085 - 0.113: 49 0.113 - 0.142: 11 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CB ILE B 560 " pdb=" CA ILE B 560 " pdb=" CG1 ILE B 560 " pdb=" CG2 ILE B 560 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CB ILE A 560 " pdb=" CA ILE A 560 " pdb=" CG1 ILE A 560 " pdb=" CG2 ILE A 560 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1043 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 526 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" CD GLU B 526 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU B 526 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 526 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 526 " 0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" CD GLU A 526 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 526 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 526 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 579 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" CG ASP A 579 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP A 579 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 579 " -0.008 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 185 2.63 - 3.20: 7118 3.20 - 3.77: 10311 3.77 - 4.33: 13524 4.33 - 4.90: 21586 Nonbonded interactions: 52724 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" OD1 ASP A 548 " model vdw 2.067 3.040 nonbonded pdb=" OG SER B 546 " pdb=" OD1 ASP B 548 " model vdw 2.068 3.040 nonbonded pdb=" O ASN B 672 " pdb=" OG1 THR B 676 " model vdw 2.103 3.040 nonbonded pdb=" O ASN A 672 " pdb=" OG1 THR A 676 " model vdw 2.103 3.040 nonbonded pdb=" O ARG B 356 " pdb=" OG SER B 359 " model vdw 2.105 3.040 ... (remaining 52719 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.550 Find NCS groups from input model: 0.120 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.006 0.044 6594 Z= 0.320 Angle : 0.864 18.061 8928 Z= 0.489 Chirality : 0.042 0.142 1046 Planarity : 0.004 0.032 1170 Dihedral : 14.117 73.918 2440 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.45 % Favored : 88.32 % Rotamer: Outliers : 1.74 % Allowed : 8.41 % Favored : 89.86 % 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: -4.55 (0.24), residues: 856 helix: -2.05 (0.22), residues: 352 sheet: -3.02 (0.39), residues: 144 loop : -3.99 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 768 HIS 0.007 0.002 HIS B 565 PHE 0.015 0.003 PHE B 706 TYR 0.009 0.001 TYR B 654 ARG 0.005 0.001 ARG B 735 Details of bonding type rmsd hydrogen bonds : bond 0.16148 ( 290) hydrogen bonds : angle 7.01021 ( 840) covalent geometry : bond 0.00621 ( 6594) covalent geometry : angle 0.86356 ( 8928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9250 (t80) cc_final: 0.8741 (t80) REVERT: A 452 LEU cc_start: 0.9225 (tp) cc_final: 0.8886 (tt) REVERT: A 481 MET cc_start: 0.8116 (mtp) cc_final: 0.7595 (mtp) REVERT: A 488 LEU cc_start: 0.9382 (tp) cc_final: 0.9141 (tp) REVERT: A 540 LEU cc_start: 0.9448 (tp) cc_final: 0.9149 (tp) REVERT: A 577 ASP cc_start: 0.8891 (t70) cc_final: 0.8655 (t0) REVERT: A 606 ILE cc_start: 0.9502 (mp) cc_final: 0.9283 (tp) REVERT: A 652 HIS cc_start: 0.9092 (t70) cc_final: 0.8428 (t70) REVERT: A 654 TYR cc_start: 0.8488 (m-80) cc_final: 0.7557 (m-10) REVERT: A 677 TYR cc_start: 0.8726 (m-80) cc_final: 0.8272 (m-80) REVERT: A 701 ASP cc_start: 0.8553 (p0) cc_final: 0.8285 (p0) REVERT: A 713 PHE cc_start: 0.8636 (m-80) cc_final: 0.8382 (m-80) REVERT: B 363 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8773 (tp40) REVERT: B 387 PHE cc_start: 0.9131 (t80) cc_final: 0.8805 (t80) REVERT: B 451 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6904 (pm20) REVERT: B 481 MET cc_start: 0.8014 (mtp) cc_final: 0.7553 (mtp) REVERT: B 488 LEU cc_start: 0.9239 (tp) cc_final: 0.8933 (tp) REVERT: B 504 GLU cc_start: 0.9233 (mt-10) cc_final: 0.9014 (pt0) REVERT: B 521 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8923 (tt) REVERT: B 582 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8809 (mmtm) REVERT: B 584 LEU cc_start: 0.9233 (mt) cc_final: 0.9020 (mt) REVERT: B 601 MET cc_start: 0.8163 (ppp) cc_final: 0.7718 (ptt) REVERT: B 606 ILE cc_start: 0.9494 (mp) cc_final: 0.9288 (tp) REVERT: B 616 PHE cc_start: 0.8115 (t80) cc_final: 0.7906 (t80) REVERT: B 620 CYS cc_start: 0.9165 (m) cc_final: 0.8922 (m) REVERT: B 654 TYR cc_start: 0.8375 (m-80) cc_final: 0.8046 (m-10) REVERT: B 677 TYR cc_start: 0.8784 (m-80) cc_final: 0.8350 (m-80) outliers start: 12 outliers final: 8 residues processed: 208 average time/residue: 0.2192 time to fit residues: 57.5352 Evaluate side-chains 146 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 369 GLN A 497 HIS A 556 GLN A 565 HIS A 599 ASN A 607 HIS A 621 ASN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 449 GLN B 497 HIS B 565 HIS B 599 ASN B 607 HIS B 621 ASN B 675 HIS ** B 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072504 restraints weight = 19868.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075029 restraints weight = 12939.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076916 restraints weight = 9554.536| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6594 Z= 0.166 Angle : 0.662 7.689 8928 Z= 0.348 Chirality : 0.044 0.146 1046 Planarity : 0.004 0.041 1170 Dihedral : 5.073 17.231 918 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: -2.94 (0.27), residues: 856 helix: -0.30 (0.26), residues: 344 sheet: -2.65 (0.40), residues: 146 loop : -3.31 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 748 HIS 0.005 0.001 HIS A 565 PHE 0.012 0.002 PHE B 760 TYR 0.005 0.001 TYR A 654 ARG 0.006 0.001 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 290) hydrogen bonds : angle 5.41903 ( 840) covalent geometry : bond 0.00364 ( 6594) covalent geometry : angle 0.66216 ( 8928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.9120 (t80) cc_final: 0.8897 (t80) REVERT: A 389 LEU cc_start: 0.9429 (pp) cc_final: 0.9214 (mp) REVERT: A 481 MET cc_start: 0.8100 (mtp) cc_final: 0.7643 (mtp) REVERT: A 488 LEU cc_start: 0.9368 (tp) cc_final: 0.9090 (tp) REVERT: A 571 HIS cc_start: 0.8430 (m90) cc_final: 0.8119 (m90) REVERT: A 574 ILE cc_start: 0.9572 (mt) cc_final: 0.9118 (tp) REVERT: A 575 ASP cc_start: 0.9125 (t0) cc_final: 0.8666 (t0) REVERT: A 677 TYR cc_start: 0.8753 (m-80) cc_final: 0.8129 (m-80) REVERT: A 713 PHE cc_start: 0.8542 (m-80) cc_final: 0.8326 (m-80) REVERT: B 363 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8537 (tp40) REVERT: B 387 PHE cc_start: 0.9042 (t80) cc_final: 0.8673 (t80) REVERT: B 451 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7090 (pm20) REVERT: B 481 MET cc_start: 0.8163 (mtp) cc_final: 0.7847 (mtp) REVERT: B 488 LEU cc_start: 0.9169 (tp) cc_final: 0.8856 (tp) REVERT: B 575 ASP cc_start: 0.9069 (t0) cc_final: 0.8544 (t0) REVERT: B 601 MET cc_start: 0.8360 (ppp) cc_final: 0.7177 (tmm) REVERT: B 654 TYR cc_start: 0.8690 (m-80) cc_final: 0.7215 (m-10) REVERT: B 677 TYR cc_start: 0.8823 (m-80) cc_final: 0.8156 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1633 time to fit residues: 41.3542 Evaluate side-chains 150 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 497 HIS A 499 ASN B 497 HIS B 499 ASN B 556 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075093 restraints weight = 19298.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077742 restraints weight = 12413.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079663 restraints weight = 9077.040| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6594 Z= 0.126 Angle : 0.608 5.921 8928 Z= 0.320 Chirality : 0.043 0.144 1046 Planarity : 0.004 0.042 1170 Dihedral : 4.686 15.705 918 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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 (0.28), residues: 856 helix: 0.22 (0.27), residues: 358 sheet: -2.27 (0.43), residues: 134 loop : -3.24 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 748 HIS 0.002 0.001 HIS A 497 PHE 0.019 0.002 PHE B 387 TYR 0.005 0.001 TYR A 654 ARG 0.004 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 290) hydrogen bonds : angle 4.93243 ( 840) covalent geometry : bond 0.00273 ( 6594) covalent geometry : angle 0.60843 ( 8928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 MET cc_start: 0.7998 (mtp) cc_final: 0.7544 (mtp) REVERT: A 488 LEU cc_start: 0.9347 (tp) cc_final: 0.9119 (tp) REVERT: A 504 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9216 (mp0) REVERT: A 534 MET cc_start: 0.8795 (tpp) cc_final: 0.8306 (tpp) REVERT: A 571 HIS cc_start: 0.8413 (m90) cc_final: 0.8072 (m90) REVERT: A 574 ILE cc_start: 0.9590 (mt) cc_final: 0.9153 (tp) REVERT: A 575 ASP cc_start: 0.9044 (t0) cc_final: 0.8654 (t0) REVERT: A 603 THR cc_start: 0.9155 (t) cc_final: 0.8646 (t) REVERT: A 658 GLU cc_start: 0.8820 (mp0) cc_final: 0.8612 (mp0) REVERT: A 677 TYR cc_start: 0.8743 (m-80) cc_final: 0.8068 (m-80) REVERT: B 363 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8751 (tp40) REVERT: B 389 LEU cc_start: 0.8848 (mp) cc_final: 0.8424 (pp) REVERT: B 451 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7335 (pm20) REVERT: B 481 MET cc_start: 0.8112 (mtp) cc_final: 0.7663 (mtp) REVERT: B 488 LEU cc_start: 0.9173 (tp) cc_final: 0.8903 (tp) REVERT: B 504 GLU cc_start: 0.9577 (pt0) cc_final: 0.9330 (pp20) REVERT: B 534 MET cc_start: 0.8637 (tpp) cc_final: 0.7922 (tpp) REVERT: B 558 LEU cc_start: 0.9189 (mt) cc_final: 0.8754 (mt) REVERT: B 571 HIS cc_start: 0.8552 (m90) cc_final: 0.8275 (m90) REVERT: B 575 ASP cc_start: 0.8952 (t0) cc_final: 0.8453 (t0) REVERT: B 582 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8762 (mmmt) REVERT: B 651 LYS cc_start: 0.9427 (mttm) cc_final: 0.9180 (mmtm) REVERT: B 654 TYR cc_start: 0.7953 (m-80) cc_final: 0.7688 (m-10) REVERT: B 677 TYR cc_start: 0.8875 (m-80) cc_final: 0.8074 (m-80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1527 time to fit residues: 38.5987 Evaluate side-chains 149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS B 497 HIS B 652 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074418 restraints weight = 19911.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077082 restraints weight = 12894.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.078999 restraints weight = 9423.297| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6594 Z= 0.146 Angle : 0.598 5.233 8928 Z= 0.312 Chirality : 0.043 0.140 1046 Planarity : 0.004 0.044 1170 Dihedral : 4.544 15.645 918 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -2.03 (0.28), residues: 856 helix: 0.53 (0.27), residues: 360 sheet: -2.19 (0.44), residues: 136 loop : -3.03 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 768 HIS 0.004 0.001 HIS A 497 PHE 0.014 0.002 PHE A 616 TYR 0.008 0.001 TYR A 654 ARG 0.003 0.000 ARG B 731 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 290) hydrogen bonds : angle 4.76216 ( 840) covalent geometry : bond 0.00316 ( 6594) covalent geometry : angle 0.59807 ( 8928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 MET cc_start: 0.7947 (mtp) cc_final: 0.7547 (mtp) REVERT: A 488 LEU cc_start: 0.9289 (tp) cc_final: 0.8993 (tp) REVERT: A 528 ILE cc_start: 0.9138 (tp) cc_final: 0.8858 (pt) REVERT: A 534 MET cc_start: 0.8794 (tpp) cc_final: 0.8297 (tpp) REVERT: A 571 HIS cc_start: 0.8486 (m90) cc_final: 0.8148 (m90) REVERT: A 574 ILE cc_start: 0.9656 (mt) cc_final: 0.9208 (tp) REVERT: A 575 ASP cc_start: 0.8918 (t0) cc_final: 0.8551 (t0) REVERT: A 654 TYR cc_start: 0.7634 (m-10) cc_final: 0.7348 (m-10) REVERT: A 677 TYR cc_start: 0.8688 (m-80) cc_final: 0.8084 (m-80) REVERT: B 363 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8272 (tp40) REVERT: B 389 LEU cc_start: 0.8995 (mp) cc_final: 0.8671 (pp) REVERT: B 481 MET cc_start: 0.8226 (mtp) cc_final: 0.7781 (mtp) REVERT: B 488 LEU cc_start: 0.9121 (tp) cc_final: 0.8785 (tp) REVERT: B 528 ILE cc_start: 0.9017 (tp) cc_final: 0.8735 (pt) REVERT: B 537 HIS cc_start: 0.8714 (m90) cc_final: 0.8390 (m90) REVERT: B 551 ARG cc_start: 0.9499 (mmm-85) cc_final: 0.9265 (mmm-85) REVERT: B 558 LEU cc_start: 0.9198 (mt) cc_final: 0.8771 (mt) REVERT: B 571 HIS cc_start: 0.8522 (m90) cc_final: 0.8225 (m90) REVERT: B 575 ASP cc_start: 0.8866 (t0) cc_final: 0.8378 (t0) REVERT: B 651 LYS cc_start: 0.9456 (mttm) cc_final: 0.9099 (mmtm) REVERT: B 677 TYR cc_start: 0.8763 (m-80) cc_final: 0.7981 (m-80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1594 time to fit residues: 37.7469 Evaluate side-chains 144 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS B 354 ASN B 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078101 restraints weight = 19340.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080863 restraints weight = 12312.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082873 restraints weight = 8877.690| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6594 Z= 0.105 Angle : 0.584 7.492 8928 Z= 0.300 Chirality : 0.042 0.139 1046 Planarity : 0.004 0.043 1170 Dihedral : 4.285 17.221 918 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -1.79 (0.29), residues: 856 helix: 0.82 (0.28), residues: 348 sheet: -2.29 (0.42), residues: 144 loop : -2.78 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 748 HIS 0.003 0.001 HIS A 497 PHE 0.009 0.001 PHE A 387 TYR 0.006 0.001 TYR B 654 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 290) hydrogen bonds : angle 4.54694 ( 840) covalent geometry : bond 0.00229 ( 6594) covalent geometry : angle 0.58438 ( 8928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LEU cc_start: 0.9371 (pp) cc_final: 0.9042 (mm) REVERT: A 451 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 481 MET cc_start: 0.7952 (mtp) cc_final: 0.7636 (mtp) REVERT: A 488 LEU cc_start: 0.9341 (tp) cc_final: 0.9138 (tp) REVERT: A 504 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8950 (tm-30) REVERT: A 528 ILE cc_start: 0.9086 (tp) cc_final: 0.8876 (pt) REVERT: A 534 MET cc_start: 0.8724 (tpp) cc_final: 0.8313 (tpp) REVERT: A 571 HIS cc_start: 0.8420 (m90) cc_final: 0.8119 (m90) REVERT: A 574 ILE cc_start: 0.9623 (mt) cc_final: 0.9155 (tp) REVERT: A 575 ASP cc_start: 0.8826 (t0) cc_final: 0.8543 (t0) REVERT: A 660 CYS cc_start: 0.8467 (m) cc_final: 0.8023 (m) REVERT: A 677 TYR cc_start: 0.8620 (m-80) cc_final: 0.8001 (m-80) REVERT: A 704 CYS cc_start: 0.8192 (p) cc_final: 0.7957 (p) REVERT: B 363 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8614 (tp40) REVERT: B 481 MET cc_start: 0.8170 (mtp) cc_final: 0.7814 (mtp) REVERT: B 488 LEU cc_start: 0.9119 (tp) cc_final: 0.8857 (tp) REVERT: B 516 GLU cc_start: 0.7185 (tt0) cc_final: 0.6856 (tt0) REVERT: B 534 MET cc_start: 0.8704 (tpp) cc_final: 0.8322 (tpp) REVERT: B 551 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9225 (mmm-85) REVERT: B 571 HIS cc_start: 0.8443 (m90) cc_final: 0.8113 (m90) REVERT: B 575 ASP cc_start: 0.8787 (t0) cc_final: 0.8277 (t0) REVERT: B 601 MET cc_start: 0.8079 (ppp) cc_final: 0.7868 (ppp) REVERT: B 660 CYS cc_start: 0.8705 (m) cc_final: 0.8244 (m) REVERT: B 677 TYR cc_start: 0.8719 (m-80) cc_final: 0.7941 (m-80) REVERT: B 704 CYS cc_start: 0.8164 (p) cc_final: 0.7927 (p) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1587 time to fit residues: 41.5303 Evaluate side-chains 147 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 681 HIS A 755 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 499 ASN B 681 HIS B 755 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075142 restraints weight = 19767.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077750 restraints weight = 12765.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079663 restraints weight = 9317.170| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6594 Z= 0.186 Angle : 0.637 7.146 8928 Z= 0.332 Chirality : 0.043 0.143 1046 Planarity : 0.004 0.045 1170 Dihedral : 4.465 15.401 918 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -2.08 (0.28), residues: 856 helix: 0.38 (0.27), residues: 372 sheet: -2.46 (0.41), residues: 146 loop : -2.90 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 768 HIS 0.010 0.001 HIS B 559 PHE 0.012 0.002 PHE A 387 TYR 0.018 0.001 TYR B 654 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 290) hydrogen bonds : angle 4.74276 ( 840) covalent geometry : bond 0.00405 ( 6594) covalent geometry : angle 0.63739 ( 8928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 481 MET cc_start: 0.8035 (mtp) cc_final: 0.7625 (mtp) REVERT: A 488 LEU cc_start: 0.9310 (tp) cc_final: 0.9002 (tp) REVERT: A 504 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 528 ILE cc_start: 0.9091 (tp) cc_final: 0.8808 (pt) REVERT: A 534 MET cc_start: 0.8699 (tpp) cc_final: 0.8280 (tpp) REVERT: A 571 HIS cc_start: 0.8469 (m90) cc_final: 0.8168 (m90) REVERT: A 574 ILE cc_start: 0.9611 (mt) cc_final: 0.9201 (tp) REVERT: A 575 ASP cc_start: 0.8884 (t0) cc_final: 0.8577 (t0) REVERT: A 654 TYR cc_start: 0.7522 (m-10) cc_final: 0.7234 (m-10) REVERT: A 660 CYS cc_start: 0.8496 (m) cc_final: 0.8057 (m) REVERT: A 677 TYR cc_start: 0.8733 (m-80) cc_final: 0.8040 (m-80) REVERT: B 353 GLU cc_start: 0.8700 (mp0) cc_final: 0.8399 (mp0) REVERT: B 389 LEU cc_start: 0.8978 (mm) cc_final: 0.8535 (pp) REVERT: B 481 MET cc_start: 0.8225 (mtp) cc_final: 0.7724 (mtp) REVERT: B 488 LEU cc_start: 0.9169 (tp) cc_final: 0.8842 (tp) REVERT: B 534 MET cc_start: 0.8710 (tpp) cc_final: 0.8048 (tpp) REVERT: B 536 ASN cc_start: 0.9020 (t0) cc_final: 0.8772 (m-40) REVERT: B 537 HIS cc_start: 0.8642 (m90) cc_final: 0.8331 (m90) REVERT: B 551 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9281 (mmm-85) REVERT: B 558 LEU cc_start: 0.9154 (mt) cc_final: 0.8797 (mt) REVERT: B 571 HIS cc_start: 0.8520 (m90) cc_final: 0.8212 (m90) REVERT: B 575 ASP cc_start: 0.8915 (t0) cc_final: 0.8444 (t0) REVERT: B 660 CYS cc_start: 0.8540 (m) cc_final: 0.8313 (m) REVERT: B 677 TYR cc_start: 0.8739 (m-80) cc_final: 0.8033 (m-80) REVERT: B 704 CYS cc_start: 0.8313 (p) cc_final: 0.8105 (p) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1522 time to fit residues: 34.7510 Evaluate side-chains 135 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 499 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 559 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075158 restraints weight = 19954.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.077752 restraints weight = 13038.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079650 restraints weight = 9588.991| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6594 Z= 0.159 Angle : 0.618 6.104 8928 Z= 0.322 Chirality : 0.044 0.157 1046 Planarity : 0.004 0.045 1170 Dihedral : 4.478 15.348 918 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.29), residues: 856 helix: 0.42 (0.27), residues: 372 sheet: -2.05 (0.43), residues: 134 loop : -2.82 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 768 HIS 0.005 0.001 HIS B 559 PHE 0.021 0.002 PHE B 616 TYR 0.009 0.001 TYR B 654 ARG 0.004 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 290) hydrogen bonds : angle 4.67996 ( 840) covalent geometry : bond 0.00352 ( 6594) covalent geometry : angle 0.61751 ( 8928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 481 MET cc_start: 0.8008 (mtp) cc_final: 0.7575 (mtp) REVERT: A 488 LEU cc_start: 0.9307 (tp) cc_final: 0.8994 (tp) REVERT: A 504 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 534 MET cc_start: 0.8684 (tpp) cc_final: 0.8189 (tpp) REVERT: A 571 HIS cc_start: 0.8397 (m90) cc_final: 0.8096 (m90) REVERT: A 575 ASP cc_start: 0.8951 (t0) cc_final: 0.8667 (t0) REVERT: A 660 CYS cc_start: 0.8455 (m) cc_final: 0.7931 (m) REVERT: A 677 TYR cc_start: 0.8692 (m-80) cc_final: 0.8053 (m-80) REVERT: B 353 GLU cc_start: 0.8712 (mp0) cc_final: 0.8328 (mp0) REVERT: B 481 MET cc_start: 0.8155 (mtp) cc_final: 0.7691 (mtp) REVERT: B 488 LEU cc_start: 0.9192 (tp) cc_final: 0.8861 (tp) REVERT: B 504 GLU cc_start: 0.9243 (pp20) cc_final: 0.9002 (pp20) REVERT: B 534 MET cc_start: 0.8750 (tpp) cc_final: 0.8340 (tpp) REVERT: B 551 ARG cc_start: 0.9459 (mmm-85) cc_final: 0.9256 (mmm-85) REVERT: B 558 LEU cc_start: 0.9162 (mt) cc_final: 0.8824 (mt) REVERT: B 571 HIS cc_start: 0.8489 (m90) cc_final: 0.8161 (m90) REVERT: B 575 ASP cc_start: 0.8979 (t0) cc_final: 0.8530 (t0) REVERT: B 660 CYS cc_start: 0.8584 (m) cc_final: 0.8354 (m) REVERT: B 677 TYR cc_start: 0.8767 (m-80) cc_final: 0.8064 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1596 time to fit residues: 36.4667 Evaluate side-chains 127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073657 restraints weight = 20177.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.076212 restraints weight = 13023.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078114 restraints weight = 9510.747| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6594 Z= 0.214 Angle : 0.676 9.063 8928 Z= 0.351 Chirality : 0.045 0.157 1046 Planarity : 0.004 0.043 1170 Dihedral : 4.731 16.489 918 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -1.97 (0.29), residues: 856 helix: 0.34 (0.28), residues: 372 sheet: -2.09 (0.42), residues: 134 loop : -2.84 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 768 HIS 0.004 0.001 HIS B 559 PHE 0.021 0.002 PHE A 616 TYR 0.015 0.002 TYR B 654 ARG 0.003 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 290) hydrogen bonds : angle 4.82938 ( 840) covalent geometry : bond 0.00467 ( 6594) covalent geometry : angle 0.67586 ( 8928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 481 MET cc_start: 0.7998 (mtp) cc_final: 0.7585 (mtp) REVERT: A 488 LEU cc_start: 0.9222 (tp) cc_final: 0.8945 (tp) REVERT: A 504 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 534 MET cc_start: 0.8823 (tpp) cc_final: 0.8372 (tpp) REVERT: A 567 GLU cc_start: 0.7169 (mp0) cc_final: 0.6682 (mp0) REVERT: A 571 HIS cc_start: 0.8430 (m90) cc_final: 0.8156 (m90) REVERT: A 575 ASP cc_start: 0.9027 (t0) cc_final: 0.8726 (t0) REVERT: A 660 CYS cc_start: 0.8529 (m) cc_final: 0.8005 (m) REVERT: A 669 GLU cc_start: 0.8822 (tt0) cc_final: 0.8608 (tt0) REVERT: A 677 TYR cc_start: 0.8768 (m-80) cc_final: 0.8053 (m-80) REVERT: A 704 CYS cc_start: 0.8311 (p) cc_final: 0.8093 (p) REVERT: B 389 LEU cc_start: 0.9020 (mm) cc_final: 0.8562 (pp) REVERT: B 481 MET cc_start: 0.8107 (mtp) cc_final: 0.7637 (mtp) REVERT: B 488 LEU cc_start: 0.9179 (tp) cc_final: 0.8885 (tp) REVERT: B 534 MET cc_start: 0.8762 (tpp) cc_final: 0.8262 (tpp) REVERT: B 571 HIS cc_start: 0.8505 (m90) cc_final: 0.8207 (m90) REVERT: B 575 ASP cc_start: 0.9049 (t0) cc_final: 0.8610 (t0) REVERT: B 601 MET cc_start: 0.8562 (ppp) cc_final: 0.7437 (tmm) REVERT: B 660 CYS cc_start: 0.8717 (m) cc_final: 0.8491 (m) REVERT: B 677 TYR cc_start: 0.8780 (m-80) cc_final: 0.8065 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1784 time to fit residues: 39.7115 Evaluate side-chains 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077208 restraints weight = 19831.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079986 restraints weight = 12693.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082045 restraints weight = 9173.084| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6594 Z= 0.124 Angle : 0.629 5.949 8928 Z= 0.325 Chirality : 0.044 0.149 1046 Planarity : 0.004 0.042 1170 Dihedral : 4.412 14.817 918 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.29), residues: 856 helix: 0.58 (0.28), residues: 360 sheet: -2.07 (0.43), residues: 134 loop : -2.63 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 748 HIS 0.003 0.001 HIS B 559 PHE 0.025 0.002 PHE B 616 TYR 0.008 0.001 TYR A 654 ARG 0.005 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 290) hydrogen bonds : angle 4.67618 ( 840) covalent geometry : bond 0.00277 ( 6594) covalent geometry : angle 0.62933 ( 8928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 LEU cc_start: 0.9312 (pp) cc_final: 0.9071 (mm) REVERT: A 451 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 481 MET cc_start: 0.7977 (mtp) cc_final: 0.7699 (mtp) REVERT: A 488 LEU cc_start: 0.9099 (tp) cc_final: 0.8847 (tp) REVERT: A 504 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8816 (tm-30) REVERT: A 534 MET cc_start: 0.8780 (tpp) cc_final: 0.8257 (tpp) REVERT: A 537 HIS cc_start: 0.8711 (m90) cc_final: 0.8477 (m90) REVERT: A 567 GLU cc_start: 0.6892 (mp0) cc_final: 0.6647 (mp0) REVERT: A 571 HIS cc_start: 0.8447 (m90) cc_final: 0.8211 (m90) REVERT: A 660 CYS cc_start: 0.8370 (m) cc_final: 0.7704 (m) REVERT: A 677 TYR cc_start: 0.8630 (m-80) cc_final: 0.8021 (m-80) REVERT: B 389 LEU cc_start: 0.8982 (mm) cc_final: 0.8512 (pp) REVERT: B 481 MET cc_start: 0.8069 (mtp) cc_final: 0.7685 (mtp) REVERT: B 488 LEU cc_start: 0.9091 (tp) cc_final: 0.8797 (tp) REVERT: B 504 GLU cc_start: 0.9121 (pp20) cc_final: 0.8784 (pp20) REVERT: B 534 MET cc_start: 0.8746 (tpp) cc_final: 0.8066 (tpp) REVERT: B 571 HIS cc_start: 0.8429 (m90) cc_final: 0.8146 (m90) REVERT: B 575 ASP cc_start: 0.8928 (t0) cc_final: 0.8561 (t0) REVERT: B 601 MET cc_start: 0.8467 (ppp) cc_final: 0.7281 (tmm) REVERT: B 651 LYS cc_start: 0.9506 (mttm) cc_final: 0.9071 (mptt) REVERT: B 660 CYS cc_start: 0.8512 (m) cc_final: 0.8236 (m) REVERT: B 677 TYR cc_start: 0.8734 (m-80) cc_final: 0.8115 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2057 time to fit residues: 47.6664 Evaluate side-chains 133 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077822 restraints weight = 19773.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080586 restraints weight = 12735.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082678 restraints weight = 9256.656| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6594 Z= 0.116 Angle : 0.627 7.898 8928 Z= 0.319 Chirality : 0.043 0.153 1046 Planarity : 0.004 0.042 1170 Dihedral : 4.251 15.777 918 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.69 (0.29), residues: 856 helix: 0.54 (0.28), residues: 360 sheet: -2.00 (0.43), residues: 134 loop : -2.53 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 748 HIS 0.003 0.001 HIS A 497 PHE 0.025 0.002 PHE A 616 TYR 0.008 0.001 TYR A 654 ARG 0.005 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 290) hydrogen bonds : angle 4.54842 ( 840) covalent geometry : bond 0.00262 ( 6594) covalent geometry : angle 0.62650 ( 8928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7603 (mp0) REVERT: A 389 LEU cc_start: 0.9333 (pp) cc_final: 0.9059 (mm) REVERT: A 481 MET cc_start: 0.8035 (mtp) cc_final: 0.7776 (mtp) REVERT: A 488 LEU cc_start: 0.9046 (tp) cc_final: 0.8799 (tp) REVERT: A 504 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8828 (tm-30) REVERT: A 534 MET cc_start: 0.8664 (tpp) cc_final: 0.8200 (tpp) REVERT: A 558 LEU cc_start: 0.8992 (mt) cc_final: 0.8756 (mp) REVERT: A 571 HIS cc_start: 0.8497 (m90) cc_final: 0.8266 (m90) REVERT: A 660 CYS cc_start: 0.8367 (m) cc_final: 0.7763 (m) REVERT: A 677 TYR cc_start: 0.8620 (m-80) cc_final: 0.8058 (m-80) REVERT: A 750 LEU cc_start: 0.9107 (tt) cc_final: 0.8832 (tp) REVERT: B 389 LEU cc_start: 0.8955 (mm) cc_final: 0.8472 (pp) REVERT: B 481 MET cc_start: 0.7870 (mtp) cc_final: 0.7577 (mtp) REVERT: B 488 LEU cc_start: 0.8952 (tp) cc_final: 0.8634 (tp) REVERT: B 504 GLU cc_start: 0.9108 (pp20) cc_final: 0.8730 (pp20) REVERT: B 534 MET cc_start: 0.8750 (tpp) cc_final: 0.8539 (tpp) REVERT: B 558 LEU cc_start: 0.9204 (mt) cc_final: 0.8945 (tt) REVERT: B 567 GLU cc_start: 0.6980 (mp0) cc_final: 0.6453 (mp0) REVERT: B 571 HIS cc_start: 0.8446 (m90) cc_final: 0.8119 (m90) REVERT: B 575 ASP cc_start: 0.8898 (t0) cc_final: 0.8536 (t0) REVERT: B 601 MET cc_start: 0.8331 (ppp) cc_final: 0.7149 (tmm) REVERT: B 651 LYS cc_start: 0.9506 (mttm) cc_final: 0.9082 (mptt) REVERT: B 660 CYS cc_start: 0.8545 (m) cc_final: 0.8231 (m) REVERT: B 677 TYR cc_start: 0.8732 (m-80) cc_final: 0.8114 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1709 time to fit residues: 41.1579 Evaluate side-chains 134 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A 556 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076452 restraints weight = 20097.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079208 restraints weight = 12776.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081259 restraints weight = 9197.764| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.125 Angle : 0.635 7.881 8928 Z= 0.325 Chirality : 0.043 0.147 1046 Planarity : 0.004 0.041 1170 Dihedral : 4.232 15.239 918 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.29), residues: 856 helix: 0.57 (0.28), residues: 360 sheet: -1.98 (0.43), residues: 134 loop : -2.48 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 748 HIS 0.005 0.001 HIS B 559 PHE 0.025 0.002 PHE B 616 TYR 0.007 0.001 TYR B 654 ARG 0.005 0.000 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 290) hydrogen bonds : angle 4.54929 ( 840) covalent geometry : bond 0.00282 ( 6594) covalent geometry : angle 0.63541 ( 8928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.55 seconds wall clock time: 39 minutes 55.64 seconds (2395.64 seconds total)