Starting phenix.real_space_refine on Sun Aug 4 08:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/08_2024/8xw3_38729.cif" } resolution = 3.63 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= 0.006 sd= 0.062 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 48 5.16 5 C 6744 2.51 5 N 1650 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 692": "OD1" <-> "OD2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 692": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.98, per 1000 atoms: 0.59 Number of scatterers: 10150 At special positions: 0 Unit cell: (91.785, 142.425, 99.17, 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 48 16.00 O 1708 8.00 N 1650 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 1.9 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 75.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.571A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.880A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.088A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 315 removed outlier: 3.669A pdb=" N ASN A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.693A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 438 removed outlier: 4.411A pdb=" N ILE A 425 " --> pdb=" O MET A 421 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 504 through 512 Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.944A pdb=" N ALA A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.615A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 removed outlier: 3.978A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.466A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 31 removed outlier: 3.571A pdb=" N GLN B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.880A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 4.088A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 290 through 315 removed outlier: 3.669A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.693A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 4.411A pdb=" N ILE B 425 " --> pdb=" O MET B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.945A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.616A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 removed outlier: 3.979A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.466A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.779A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.779A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2067 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: 3.16 Time building geometry restraints manager: 4.37 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: 3011 1.34 - 1.46: 1764 1.46 - 1.58: 5577 1.58 - 1.70: 0 1.70 - 1.81: 88 Bond restraints: 10440 Sorted by residual: bond pdb=" CB VAL B 476 " pdb=" CG1 VAL B 476 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.52e+00 bond pdb=" CB VAL A 476 " pdb=" CG1 VAL A 476 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG LEU B 579 " pdb=" CD2 LEU B 579 " 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 579 " pdb=" CD2 LEU A 579 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " ideal model delta sigma weight residual 1.528 1.510 0.017 1.39e-02 5.18e+03 1.56e+00 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.49: 252 105.49 - 112.63: 5461 112.63 - 119.76: 3356 119.76 - 126.89: 4973 126.89 - 134.03: 158 Bond angle restraints: 14200 Sorted by residual: angle pdb=" C PHE B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta sigma weight residual 123.11 117.16 5.95 1.42e+00 4.96e-01 1.76e+01 angle pdb=" C PHE A 451 " pdb=" N GLU A 452 " pdb=" CA GLU A 452 " ideal model delta sigma weight residual 123.11 117.19 5.92 1.42e+00 4.96e-01 1.74e+01 angle pdb=" CA GLU B 452 " pdb=" CB GLU B 452 " pdb=" CG GLU B 452 " ideal model delta sigma weight residual 114.10 107.63 6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " ideal model delta sigma weight residual 114.10 107.64 6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" N TRP A 42 " pdb=" CA TRP A 42 " pdb=" C TRP A 42 " ideal model delta sigma weight residual 113.72 109.33 4.39 1.52e+00 4.33e-01 8.35e+00 ... (remaining 14195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 5510 16.44 - 32.88: 490 32.88 - 49.33: 102 49.33 - 65.77: 16 65.77 - 82.21: 10 Dihedral angle restraints: 6128 sinusoidal: 2386 harmonic: 3742 Sorted by residual: dihedral pdb=" CA GLU B 452 " pdb=" C GLU B 452 " pdb=" N GLY B 453 " pdb=" CA GLY B 453 " ideal model delta harmonic sigma weight residual -180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLU A 452 " pdb=" C GLU A 452 " pdb=" N GLY A 453 " pdb=" CA GLY A 453 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASN A 475 " pdb=" C ASN A 475 " pdb=" N VAL A 476 " pdb=" CA VAL A 476 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 795 0.026 - 0.052: 470 0.052 - 0.078: 187 0.078 - 0.103: 99 0.103 - 0.129: 53 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA THR A 455 " pdb=" N THR A 455 " pdb=" C THR A 455 " pdb=" CB THR A 455 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA PRO B 77 " pdb=" N PRO B 77 " pdb=" C PRO B 77 " pdb=" CB PRO B 77 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA THR B 455 " pdb=" N THR B 455 " pdb=" C THR B 455 " pdb=" CB THR B 455 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1601 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 677 " 0.033 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO B 678 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 678 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 678 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 677 " -0.033 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 678 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 678 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 678 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 472 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASN B 472 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN B 472 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 473 " 0.010 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 101 2.65 - 3.21: 9992 3.21 - 3.77: 16258 3.77 - 4.34: 20568 4.34 - 4.90: 34305 Nonbonded interactions: 81224 Sorted by model distance: nonbonded pdb=" O PRO B 354 " pdb=" OH TYR B 712 " model vdw 2.085 3.040 nonbonded pdb=" O PRO A 354 " pdb=" OH TYR A 712 " model vdw 2.085 3.040 nonbonded pdb=" NH2 ARG A 198 " pdb=" OD2 ASP A 200 " model vdw 2.258 3.120 nonbonded pdb=" NH2 ARG B 198 " pdb=" OD2 ASP B 200 " model vdw 2.259 3.120 nonbonded pdb=" O GLU A 195 " pdb=" NZ LYS A 691 " model vdw 2.293 3.120 ... (remaining 81219 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' 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.790 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.052 10440 Z= 0.339 Angle : 0.728 7.529 14200 Z= 0.399 Chirality : 0.044 0.129 1604 Planarity : 0.005 0.049 1762 Dihedral : 13.288 82.211 3696 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.53 (0.24), residues: 1248 helix: 2.11 (0.17), residues: 868 sheet: -0.96 (0.85), residues: 36 loop : -1.74 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 525 HIS 0.004 0.001 HIS B 542 PHE 0.022 0.002 PHE A 420 TYR 0.016 0.002 TYR A 468 ARG 0.007 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.158 Fit side-chains REVERT: A 6 ASP cc_start: 0.7783 (m-30) cc_final: 0.7546 (m-30) REVERT: A 521 MET cc_start: 0.8796 (tpp) cc_final: 0.8593 (tpp) REVERT: B 395 PHE cc_start: 0.8530 (t80) cc_final: 0.8217 (t80) REVERT: B 525 TRP cc_start: 0.8991 (m-10) cc_final: 0.8661 (m-10) REVERT: B 536 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7352 (mmtt) REVERT: B 613 TYR cc_start: 0.7954 (m-10) cc_final: 0.7747 (m-10) REVERT: B 672 CYS cc_start: 0.9031 (m) cc_final: 0.8709 (m) REVERT: B 689 MET cc_start: 0.9224 (tpt) cc_final: 0.8994 (tpt) REVERT: B 699 GLU cc_start: 0.8354 (mp0) cc_final: 0.8003 (mp0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1694 time to fit residues: 54.6075 Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 397 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10440 Z= 0.212 Angle : 0.603 6.791 14200 Z= 0.302 Chirality : 0.042 0.164 1604 Planarity : 0.005 0.055 1762 Dihedral : 4.261 18.959 1360 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.70 % Allowed : 7.94 % Favored : 90.36 % 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: 1.73 (0.25), residues: 1248 helix: 2.21 (0.17), residues: 872 sheet: -0.33 (0.92), residues: 30 loop : -1.60 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 624 HIS 0.002 0.001 HIS B 90 PHE 0.020 0.001 PHE A 471 TYR 0.015 0.001 TYR A 468 ARG 0.004 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7857 (m-30) cc_final: 0.7584 (m-30) REVERT: A 521 MET cc_start: 0.8843 (tpp) cc_final: 0.8606 (tpp) REVERT: A 574 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8910 (mm-40) REVERT: B 200 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 395 PHE cc_start: 0.8499 (t80) cc_final: 0.8199 (t80) REVERT: B 511 MET cc_start: 0.6960 (mmm) cc_final: 0.6583 (mmm) REVERT: B 540 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8161 (tmm) REVERT: B 661 LEU cc_start: 0.8918 (mt) cc_final: 0.8695 (mt) REVERT: B 672 CYS cc_start: 0.9020 (m) cc_final: 0.8685 (m) REVERT: B 677 GLU cc_start: 0.7979 (tt0) cc_final: 0.7739 (tt0) REVERT: B 689 MET cc_start: 0.9220 (tpt) cc_final: 0.8993 (tpt) REVERT: B 699 GLU cc_start: 0.8421 (mp0) cc_final: 0.8179 (mp0) outliers start: 18 outliers final: 7 residues processed: 195 average time/residue: 0.1808 time to fit residues: 52.7823 Evaluate side-chains 178 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 574 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10440 Z= 0.178 Angle : 0.583 12.621 14200 Z= 0.285 Chirality : 0.041 0.154 1604 Planarity : 0.004 0.056 1762 Dihedral : 4.069 17.690 1360 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 10.78 % Favored : 87.15 % 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 (0.25), residues: 1248 helix: 2.24 (0.17), residues: 874 sheet: 0.40 (0.96), residues: 36 loop : -1.68 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.000 HIS B 379 PHE 0.022 0.001 PHE A 471 TYR 0.020 0.001 TYR A 368 ARG 0.006 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.232 Fit side-chains REVERT: A 6 ASP cc_start: 0.7841 (m-30) cc_final: 0.7557 (m-30) REVERT: A 30 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 689 MET cc_start: 0.9158 (tpt) cc_final: 0.8930 (tpp) REVERT: B 164 VAL cc_start: 0.9209 (t) cc_final: 0.8952 (p) REVERT: B 383 PHE cc_start: 0.8775 (t80) cc_final: 0.8564 (t80) REVERT: B 387 PHE cc_start: 0.8411 (t80) cc_final: 0.8067 (t80) REVERT: B 395 PHE cc_start: 0.8455 (t80) cc_final: 0.8188 (t80) REVERT: B 470 ILE cc_start: 0.9020 (tp) cc_final: 0.8647 (tt) REVERT: B 511 MET cc_start: 0.7089 (mmm) cc_final: 0.6666 (mmm) REVERT: B 677 GLU cc_start: 0.7919 (tt0) cc_final: 0.7663 (tt0) REVERT: B 689 MET cc_start: 0.9198 (tpt) cc_final: 0.8973 (tpt) outliers start: 22 outliers final: 13 residues processed: 191 average time/residue: 0.1776 time to fit residues: 51.1335 Evaluate side-chains 182 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10440 Z= 0.201 Angle : 0.581 10.108 14200 Z= 0.286 Chirality : 0.041 0.165 1604 Planarity : 0.004 0.056 1762 Dihedral : 3.961 17.324 1360 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.02 % Allowed : 10.68 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1248 helix: 2.25 (0.17), residues: 874 sheet: 0.16 (0.89), residues: 46 loop : -1.83 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.003 0.001 HIS A 379 PHE 0.018 0.001 PHE A 471 TYR 0.015 0.001 TYR A 181 ARG 0.007 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.166 Fit side-chains REVERT: A 6 ASP cc_start: 0.7799 (m-30) cc_final: 0.7512 (m-30) REVERT: A 30 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 448 MET cc_start: 0.7290 (ttm) cc_final: 0.6642 (tpt) REVERT: A 470 ILE cc_start: 0.9093 (tp) cc_final: 0.8891 (tp) REVERT: A 677 GLU cc_start: 0.8078 (tt0) cc_final: 0.7815 (mt-10) REVERT: A 689 MET cc_start: 0.9171 (tpt) cc_final: 0.8941 (tpp) REVERT: B 383 PHE cc_start: 0.8767 (t80) cc_final: 0.8480 (t80) REVERT: B 387 PHE cc_start: 0.8380 (t80) cc_final: 0.8092 (t80) REVERT: B 525 TRP cc_start: 0.8846 (m-10) cc_final: 0.8457 (m-10) REVERT: B 531 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 661 LEU cc_start: 0.8892 (mt) cc_final: 0.8673 (mt) REVERT: B 672 CYS cc_start: 0.9045 (m) cc_final: 0.8620 (m) REVERT: B 677 GLU cc_start: 0.8013 (tt0) cc_final: 0.7757 (tt0) REVERT: B 689 MET cc_start: 0.9210 (tpt) cc_final: 0.9008 (tpt) outliers start: 32 outliers final: 24 residues processed: 195 average time/residue: 0.1599 time to fit residues: 48.4695 Evaluate side-chains 194 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 0.1980 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10440 Z= 0.249 Angle : 0.591 9.474 14200 Z= 0.294 Chirality : 0.042 0.169 1604 Planarity : 0.005 0.057 1762 Dihedral : 3.988 18.698 1360 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.84 % Allowed : 11.81 % Favored : 85.35 % 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: 1.77 (0.25), residues: 1248 helix: 2.27 (0.17), residues: 874 sheet: 0.38 (0.88), residues: 44 loop : -1.90 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.003 0.001 HIS B 90 PHE 0.015 0.001 PHE A 577 TYR 0.019 0.001 TYR A 181 ARG 0.007 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.215 Fit side-chains REVERT: A 6 ASP cc_start: 0.7792 (m-30) cc_final: 0.7513 (m-30) REVERT: A 30 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 93 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 689 MET cc_start: 0.9183 (tpt) cc_final: 0.8959 (tpp) REVERT: B 383 PHE cc_start: 0.8781 (t80) cc_final: 0.8505 (t80) REVERT: B 448 MET cc_start: 0.7590 (ttp) cc_final: 0.7040 (tpt) REVERT: B 525 TRP cc_start: 0.8812 (m-10) cc_final: 0.8532 (m-10) REVERT: B 531 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 540 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8234 (tmm) REVERT: B 672 CYS cc_start: 0.9058 (m) cc_final: 0.8605 (m) REVERT: B 677 GLU cc_start: 0.8089 (tt0) cc_final: 0.7828 (tt0) outliers start: 30 outliers final: 23 residues processed: 183 average time/residue: 0.1602 time to fit residues: 45.6489 Evaluate side-chains 192 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10440 Z= 0.173 Angle : 0.575 9.229 14200 Z= 0.283 Chirality : 0.041 0.178 1604 Planarity : 0.004 0.056 1762 Dihedral : 3.908 18.258 1360 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 13.33 % Favored : 84.12 % 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: 1.80 (0.25), residues: 1248 helix: 2.28 (0.17), residues: 876 sheet: 0.06 (0.86), residues: 46 loop : -1.80 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.003 0.000 HIS B 379 PHE 0.017 0.001 PHE A 395 TYR 0.011 0.001 TYR B 181 ARG 0.006 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.123 Fit side-chains REVERT: A 30 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 448 MET cc_start: 0.7148 (ttm) cc_final: 0.6700 (tpp) REVERT: A 511 MET cc_start: 0.7412 (mmm) cc_final: 0.6823 (mmm) REVERT: A 677 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 689 MET cc_start: 0.9166 (tpt) cc_final: 0.8935 (tpp) REVERT: B 19 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 164 VAL cc_start: 0.9187 (t) cc_final: 0.8916 (p) REVERT: B 383 PHE cc_start: 0.8792 (t80) cc_final: 0.8503 (t80) REVERT: B 387 PHE cc_start: 0.8361 (t80) cc_final: 0.8014 (t80) REVERT: B 448 MET cc_start: 0.7584 (ttp) cc_final: 0.6628 (tpt) REVERT: B 521 MET cc_start: 0.8910 (tpp) cc_final: 0.8023 (mmt) REVERT: B 525 TRP cc_start: 0.8731 (m-10) cc_final: 0.7962 (m-10) REVERT: B 531 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 540 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8220 (tmm) REVERT: B 677 GLU cc_start: 0.8037 (tt0) cc_final: 0.7791 (tt0) outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 0.1640 time to fit residues: 47.5980 Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10440 Z= 0.201 Angle : 0.611 14.391 14200 Z= 0.293 Chirality : 0.042 0.183 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.887 17.619 1360 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.27 % Allowed : 14.27 % Favored : 83.46 % 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: 1.77 (0.25), residues: 1248 helix: 2.25 (0.17), residues: 876 sheet: -0.02 (0.85), residues: 46 loop : -1.80 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.003 0.000 HIS B 379 PHE 0.020 0.001 PHE A 471 TYR 0.020 0.001 TYR B 368 ARG 0.006 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.166 Fit side-chains REVERT: A 30 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 511 MET cc_start: 0.7458 (mmm) cc_final: 0.6854 (mmm) REVERT: A 521 MET cc_start: 0.8748 (tpp) cc_final: 0.8497 (tpp) REVERT: A 677 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 689 MET cc_start: 0.9177 (tpt) cc_final: 0.8946 (tpp) REVERT: B 19 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 387 PHE cc_start: 0.8434 (t80) cc_final: 0.8049 (t80) REVERT: B 525 TRP cc_start: 0.8714 (m-10) cc_final: 0.8468 (m-10) REVERT: B 531 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 677 GLU cc_start: 0.8072 (tt0) cc_final: 0.7826 (tt0) outliers start: 24 outliers final: 17 residues processed: 175 average time/residue: 0.1598 time to fit residues: 43.6761 Evaluate side-chains 184 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10440 Z= 0.187 Angle : 0.607 11.444 14200 Z= 0.291 Chirality : 0.041 0.196 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.840 18.197 1360 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.36 % Allowed : 14.74 % Favored : 82.89 % 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: 1.78 (0.25), residues: 1248 helix: 2.25 (0.17), residues: 876 sheet: 0.23 (0.86), residues: 44 loop : -1.80 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.000 HIS B 379 PHE 0.017 0.001 PHE B 471 TYR 0.013 0.001 TYR B 181 ARG 0.007 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.150 Fit side-chains REVERT: A 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8678 (mm) REVERT: A 521 MET cc_start: 0.8775 (tpp) cc_final: 0.8477 (tpp) REVERT: A 534 MET cc_start: 0.8315 (mtt) cc_final: 0.8051 (mtt) REVERT: A 677 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: A 689 MET cc_start: 0.9173 (tpt) cc_final: 0.8943 (tpp) REVERT: B 19 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: B 387 PHE cc_start: 0.8439 (t80) cc_final: 0.8079 (t80) REVERT: B 521 MET cc_start: 0.8749 (tpp) cc_final: 0.8114 (mmt) REVERT: B 525 TRP cc_start: 0.8631 (m-10) cc_final: 0.8046 (m-10) REVERT: B 531 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 677 GLU cc_start: 0.8011 (tt0) cc_final: 0.7790 (tt0) outliers start: 25 outliers final: 18 residues processed: 175 average time/residue: 0.1593 time to fit residues: 43.4850 Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0170 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10440 Z= 0.172 Angle : 0.615 11.216 14200 Z= 0.293 Chirality : 0.041 0.203 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.815 17.398 1360 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.61 % Allowed : 15.69 % Favored : 82.70 % 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: 1.77 (0.25), residues: 1248 helix: 2.24 (0.17), residues: 876 sheet: -0.11 (0.83), residues: 46 loop : -1.74 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.002 0.000 HIS B 379 PHE 0.018 0.001 PHE B 471 TYR 0.026 0.001 TYR A 368 ARG 0.006 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.184 Fit side-chains REVERT: A 30 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 521 MET cc_start: 0.8783 (tpp) cc_final: 0.8441 (tpp) REVERT: A 534 MET cc_start: 0.8267 (mtt) cc_final: 0.8033 (mtt) REVERT: A 689 MET cc_start: 0.9170 (tpt) cc_final: 0.8939 (tpp) REVERT: B 387 PHE cc_start: 0.8389 (t80) cc_final: 0.8036 (t80) REVERT: B 521 MET cc_start: 0.8788 (tpp) cc_final: 0.8035 (mmt) REVERT: B 525 TRP cc_start: 0.8676 (m-10) cc_final: 0.8047 (m-10) REVERT: B 531 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 677 GLU cc_start: 0.7988 (tt0) cc_final: 0.7771 (tt0) outliers start: 17 outliers final: 13 residues processed: 172 average time/residue: 0.1645 time to fit residues: 43.6641 Evaluate side-chains 175 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10440 Z= 0.225 Angle : 0.628 10.718 14200 Z= 0.301 Chirality : 0.042 0.202 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.831 18.447 1360 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.61 % Allowed : 16.16 % Favored : 82.23 % 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: 1.77 (0.25), residues: 1248 helix: 2.28 (0.17), residues: 874 sheet: 0.03 (0.86), residues: 44 loop : -1.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 624 HIS 0.003 0.001 HIS B 379 PHE 0.018 0.001 PHE B 471 TYR 0.021 0.001 TYR B 469 ARG 0.006 0.000 ARG B 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.317 Fit side-chains REVERT: A 30 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 689 MET cc_start: 0.9184 (tpt) cc_final: 0.8957 (tpp) REVERT: B 387 PHE cc_start: 0.8467 (t80) cc_final: 0.8082 (t80) REVERT: B 521 MET cc_start: 0.8766 (tpp) cc_final: 0.8027 (mmt) REVERT: B 525 TRP cc_start: 0.8673 (m-10) cc_final: 0.8063 (m-10) REVERT: B 531 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 649 LYS cc_start: 0.4800 (tptp) cc_final: 0.4598 (mmmt) REVERT: B 677 GLU cc_start: 0.8059 (tt0) cc_final: 0.7842 (tt0) outliers start: 17 outliers final: 14 residues processed: 162 average time/residue: 0.1851 time to fit residues: 46.5232 Evaluate side-chains 170 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088562 restraints weight = 19622.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091324 restraints weight = 10335.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.093103 restraints weight = 7036.853| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10440 Z= 0.187 Angle : 0.616 10.750 14200 Z= 0.296 Chirality : 0.042 0.203 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.828 18.229 1360 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 16.16 % Favored : 82.33 % 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: 1.75 (0.25), residues: 1248 helix: 2.20 (0.17), residues: 888 sheet: 0.01 (0.87), residues: 44 loop : -1.83 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.003 0.000 HIS B 379 PHE 0.018 0.001 PHE B 471 TYR 0.027 0.001 TYR B 368 ARG 0.005 0.000 ARG B 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.66 seconds wall clock time: 34 minutes 54.42 seconds (2094.42 seconds total)