Starting phenix.real_space_refine on Wed Jun 26 12:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/06_2024/8xw3_38729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/06_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_38729/06_2024/8xw3_38729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/06_2024/8xw3_38729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/06_2024/8xw3_38729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw3_38729/06_2024/8xw3_38729.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 6.02, 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: 4.23 Conformation dependent library (CDL) restraints added in 1.6 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: 0.88 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: 2.68 Time building geometry restraints manager: 4.61 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 2.440 nonbonded pdb=" O PRO A 354 " pdb=" OH TYR A 712 " model vdw 2.085 2.440 nonbonded pdb=" NH2 ARG A 198 " pdb=" OD2 ASP A 200 " model vdw 2.258 2.520 nonbonded pdb=" NH2 ARG B 198 " pdb=" OD2 ASP B 200 " model vdw 2.259 2.520 nonbonded pdb=" O GLU A 195 " pdb=" NZ LYS A 691 " model vdw 2.293 2.520 ... (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 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.180 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.660 Find NCS groups from input model: 0.480 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- 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: 0.1691 time to fit residues: 54.5998 Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10440 Z= 0.200 Angle : 0.591 6.864 14200 Z= 0.296 Chirality : 0.041 0.165 1604 Planarity : 0.004 0.052 1762 Dihedral : 4.250 18.906 1360 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.61 % Allowed : 7.56 % Favored : 90.83 % 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: 2.24 (0.17), residues: 872 sheet: -0.24 (0.94), residues: 30 loop : -1.63 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 624 HIS 0.002 0.001 HIS A 379 PHE 0.020 0.001 PHE A 471 TYR 0.015 0.001 TYR A 468 ARG 0.003 0.000 ARG B 375 *********************** 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 203 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.105 Fit side-chains REVERT: A 6 ASP cc_start: 0.7756 (m-30) cc_final: 0.7509 (m-30) REVERT: A 521 MET cc_start: 0.8843 (tpp) cc_final: 0.8611 (tpp) REVERT: B 200 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 395 PHE cc_start: 0.8504 (t80) cc_final: 0.8198 (t80) REVERT: B 511 MET cc_start: 0.6967 (mmm) cc_final: 0.6589 (mmm) REVERT: B 540 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8133 (tmm) REVERT: B 661 LEU cc_start: 0.8938 (mt) cc_final: 0.8718 (mt) REVERT: B 672 CYS cc_start: 0.9013 (m) cc_final: 0.8674 (m) REVERT: B 677 GLU cc_start: 0.7995 (tt0) cc_final: 0.7793 (tt0) REVERT: B 689 MET cc_start: 0.9197 (tpt) cc_final: 0.8964 (tpt) REVERT: B 699 GLU cc_start: 0.8300 (mp0) cc_final: 0.7982 (mp0) outliers start: 17 outliers final: 7 residues processed: 190 average time/residue: 0.1675 time to fit residues: 48.5235 Evaluate side-chains 174 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE 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 641 LEU 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: 0.6980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1460 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= 0.202 Angle : 0.590 13.149 14200 Z= 0.289 Chirality : 0.041 0.155 1604 Planarity : 0.004 0.056 1762 Dihedral : 4.062 17.996 1360 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.98 % Allowed : 10.49 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1248 helix: 2.26 (0.17), residues: 874 sheet: 0.25 (0.95), residues: 36 loop : -1.77 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.002 0.001 HIS A 90 PHE 0.022 0.001 PHE A 471 TYR 0.017 0.001 TYR A 368 ARG 0.003 0.000 ARG B 375 *********************** 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 197 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.126 Fit side-chains REVERT: A 6 ASP cc_start: 0.7737 (m-30) cc_final: 0.7380 (m-30) REVERT: A 689 MET cc_start: 0.9142 (tpt) cc_final: 0.8916 (tpp) REVERT: B 383 PHE cc_start: 0.8776 (t80) cc_final: 0.8560 (t80) REVERT: B 395 PHE cc_start: 0.8518 (t80) cc_final: 0.8222 (t80) REVERT: B 470 ILE cc_start: 0.9046 (tp) cc_final: 0.8650 (tt) REVERT: B 511 MET cc_start: 0.7111 (mmm) cc_final: 0.6683 (mmm) REVERT: B 531 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 677 GLU cc_start: 0.8019 (tt0) cc_final: 0.7765 (tt0) REVERT: B 689 MET cc_start: 0.9184 (tpt) cc_final: 0.8938 (tpt) REVERT: B 699 GLU cc_start: 0.8289 (mp0) cc_final: 0.7955 (mp0) outliers start: 21 outliers final: 12 residues processed: 183 average time/residue: 0.1760 time to fit residues: 48.2463 Evaluate side-chains 173 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 94 ASP 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 641 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 436 LEU 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: 0.6980 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1710 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= 0.176 Angle : 0.566 9.993 14200 Z= 0.278 Chirality : 0.040 0.167 1604 Planarity : 0.004 0.056 1762 Dihedral : 3.955 17.365 1360 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.65 % Allowed : 11.34 % Favored : 86.01 % 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: 1.88 (0.25), residues: 1248 helix: 2.32 (0.17), residues: 874 sheet: 0.61 (1.03), residues: 36 loop : -1.72 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.002 0.000 HIS B 90 PHE 0.018 0.001 PHE A 471 TYR 0.012 0.001 TYR A 181 ARG 0.004 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 204 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.203 Fit side-chains REVERT: A 6 ASP cc_start: 0.7701 (m-30) cc_final: 0.7471 (m-30) REVERT: A 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8588 (mm) REVERT: A 426 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7739 (pp30) REVERT: A 448 MET cc_start: 0.7302 (ttm) cc_final: 0.6685 (tpt) REVERT: A 689 MET cc_start: 0.9151 (tpt) cc_final: 0.8923 (tpp) REVERT: B 164 VAL cc_start: 0.9202 (t) cc_final: 0.8949 (p) REVERT: B 383 PHE cc_start: 0.8774 (t80) cc_final: 0.8505 (t80) REVERT: B 387 PHE cc_start: 0.8380 (t80) cc_final: 0.8115 (t80) REVERT: B 395 PHE cc_start: 0.8495 (t80) cc_final: 0.8233 (t80) REVERT: B 521 MET cc_start: 0.8841 (tpp) cc_final: 0.8176 (mmt) REVERT: B 525 TRP cc_start: 0.8841 (m-10) cc_final: 0.8504 (m-10) REVERT: B 531 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 540 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8170 (tmm) REVERT: B 661 LEU cc_start: 0.8911 (mt) cc_final: 0.8710 (mt) REVERT: B 677 GLU cc_start: 0.7998 (tt0) cc_final: 0.7751 (tt0) REVERT: B 689 MET cc_start: 0.9160 (tpt) cc_final: 0.8914 (tpt) REVERT: B 699 GLU cc_start: 0.8250 (mp0) cc_final: 0.7927 (mp0) outliers start: 28 outliers final: 17 residues processed: 186 average time/residue: 0.1720 time to fit residues: 48.7833 Evaluate side-chains 183 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 373 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 540 MET 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: 3.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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** B 14 ASN B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10440 Z= 0.271 Angle : 0.604 9.260 14200 Z= 0.298 Chirality : 0.042 0.171 1604 Planarity : 0.005 0.057 1762 Dihedral : 3.990 18.067 1360 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.55 % Allowed : 11.81 % Favored : 85.63 % 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: 2.31 (0.17), residues: 874 sheet: -0.19 (0.86), residues: 46 loop : -1.92 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 624 HIS 0.004 0.001 HIS B 90 PHE 0.014 0.001 PHE A 577 TYR 0.021 0.001 TYR A 181 ARG 0.004 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 193 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.227 Fit side-chains REVERT: A 6 ASP cc_start: 0.7696 (m-30) cc_final: 0.7397 (m-30) REVERT: A 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8632 (mm) REVERT: A 93 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (tt) REVERT: A 448 MET cc_start: 0.7219 (ttm) cc_final: 0.6645 (tpt) REVERT: A 689 MET cc_start: 0.9171 (tpt) cc_final: 0.8940 (tpp) REVERT: B 383 PHE cc_start: 0.8790 (t80) cc_final: 0.8507 (t80) REVERT: B 387 PHE cc_start: 0.8488 (t80) cc_final: 0.8166 (t80) REVERT: B 395 PHE cc_start: 0.8550 (t80) cc_final: 0.8247 (t80) REVERT: B 531 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 672 CYS cc_start: 0.9053 (m) cc_final: 0.8717 (m) REVERT: B 677 GLU cc_start: 0.8124 (tt0) cc_final: 0.7873 (tt0) REVERT: B 699 GLU cc_start: 0.8266 (mp0) cc_final: 0.7955 (mp0) outliers start: 27 outliers final: 21 residues processed: 175 average time/residue: 0.1580 time to fit residues: 43.3753 Evaluate side-chains 181 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 94 ASP 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 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 432 ILE Chi-restraints excluded: chain B residue 436 LEU 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: 3.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10440 Z= 0.222 Angle : 0.578 9.108 14200 Z= 0.286 Chirality : 0.041 0.174 1604 Planarity : 0.004 0.056 1762 Dihedral : 3.959 17.632 1360 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.65 % Allowed : 12.95 % Favored : 84.40 % 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: 2.30 (0.17), residues: 876 sheet: -0.31 (0.84), residues: 46 loop : -1.89 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.003 0.001 HIS B 90 PHE 0.015 0.001 PHE A 395 TYR 0.016 0.001 TYR B 368 ARG 0.003 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 203 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.218 Fit side-chains REVERT: A 30 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 574 GLN cc_start: 0.9192 (mm110) cc_final: 0.8962 (mm-40) REVERT: A 657 PHE cc_start: 0.8625 (m-80) cc_final: 0.8392 (m-10) REVERT: A 689 MET cc_start: 0.9172 (tpt) cc_final: 0.8941 (tpp) REVERT: B 19 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 383 PHE cc_start: 0.8792 (t80) cc_final: 0.8503 (t80) REVERT: B 395 PHE cc_start: 0.8595 (t80) cc_final: 0.8289 (t80) REVERT: B 525 TRP cc_start: 0.8896 (m-10) cc_final: 0.8483 (m-10) REVERT: B 531 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 677 GLU cc_start: 0.8110 (tt0) cc_final: 0.7848 (tt0) outliers start: 28 outliers final: 18 residues processed: 182 average time/residue: 0.1627 time to fit residues: 46.3156 Evaluate side-chains 186 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 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 94 ASP Chi-restraints excluded: chain A residue 173 THR 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 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 99 LEU 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 590 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 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: 0.0970 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2139 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 : 0.601 14.142 14200 Z= 0.287 Chirality : 0.041 0.188 1604 Planarity : 0.004 0.055 1762 Dihedral : 3.905 18.103 1360 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.08 % 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: 2.29 (0.17), residues: 876 sheet: -0.27 (0.85), residues: 46 loop : -1.86 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.001 0.000 HIS B 90 PHE 0.014 0.001 PHE B 577 TYR 0.025 0.001 TYR B 368 ARG 0.003 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 202 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.153 Fit side-chains REVERT: A 7 ILE cc_start: 0.9174 (mm) cc_final: 0.8921 (mm) REVERT: A 30 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 448 MET cc_start: 0.7264 (ttm) cc_final: 0.6656 (tpt) REVERT: A 689 MET cc_start: 0.9155 (tpt) cc_final: 0.8923 (tpp) REVERT: B 19 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: B 164 VAL cc_start: 0.9191 (t) cc_final: 0.8924 (p) REVERT: B 387 PHE cc_start: 0.8366 (t80) cc_final: 0.7969 (t80) REVERT: B 395 PHE cc_start: 0.8542 (t80) cc_final: 0.8249 (t80) REVERT: B 531 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 661 LEU cc_start: 0.8749 (mt) cc_final: 0.8541 (mt) REVERT: B 677 GLU cc_start: 0.8039 (tt0) cc_final: 0.7811 (tt0) outliers start: 22 outliers final: 16 residues processed: 184 average time/residue: 0.1583 time to fit residues: 44.7417 Evaluate side-chains 187 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 482 ILE 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 165 MET 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 436 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2193 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= 0.209 Angle : 0.621 11.428 14200 Z= 0.296 Chirality : 0.041 0.192 1604 Planarity : 0.004 0.054 1762 Dihedral : 3.872 17.295 1360 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 15.41 % 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: 1.76 (0.25), residues: 1248 helix: 2.29 (0.17), residues: 874 sheet: -0.40 (0.82), residues: 46 loop : -1.85 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.002 0.000 HIS B 90 PHE 0.025 0.001 PHE A 471 TYR 0.021 0.001 TYR A 368 ARG 0.003 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 191 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.208 Fit side-chains REVERT: A 7 ILE cc_start: 0.9240 (mm) cc_final: 0.9038 (mm) REVERT: A 30 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8642 (mm) REVERT: A 448 MET cc_start: 0.7304 (ttm) cc_final: 0.6641 (tpt) REVERT: A 689 MET cc_start: 0.9170 (tpt) cc_final: 0.8940 (tpp) REVERT: B 19 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: B 387 PHE cc_start: 0.8414 (t80) cc_final: 0.8040 (t80) REVERT: B 395 PHE cc_start: 0.8570 (t80) cc_final: 0.8257 (t80) REVERT: B 521 MET cc_start: 0.8890 (tpp) cc_final: 0.8029 (mmt) REVERT: B 525 TRP cc_start: 0.8817 (m-10) cc_final: 0.8056 (m-10) REVERT: B 531 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 661 LEU cc_start: 0.8765 (mt) cc_final: 0.8534 (mt) REVERT: B 677 GLU cc_start: 0.8085 (tt0) cc_final: 0.7830 (tt0) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.1657 time to fit residues: 44.1154 Evaluate side-chains 179 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 373 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10440 Z= 0.197 Angle : 0.617 11.300 14200 Z= 0.297 Chirality : 0.041 0.196 1604 Planarity : 0.004 0.054 1762 Dihedral : 3.859 17.979 1360 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.98 % Allowed : 16.07 % Favored : 81.95 % 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: 1.81 (0.25), residues: 1248 helix: 2.31 (0.17), residues: 876 sheet: -0.11 (0.84), residues: 44 loop : -1.82 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 624 HIS 0.002 0.000 HIS B 90 PHE 0.021 0.001 PHE B 471 TYR 0.013 0.001 TYR B 181 ARG 0.003 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 184 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.211 Fit side-chains REVERT: A 30 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 521 MET cc_start: 0.8734 (tpp) cc_final: 0.8477 (tpp) REVERT: A 689 MET cc_start: 0.9165 (tpt) cc_final: 0.8931 (tpp) REVERT: B 387 PHE cc_start: 0.8429 (t80) cc_final: 0.8062 (t80) REVERT: B 525 TRP cc_start: 0.8860 (m-10) cc_final: 0.8607 (m-10) REVERT: B 661 LEU cc_start: 0.8786 (mt) cc_final: 0.8550 (mt) REVERT: B 677 GLU cc_start: 0.8077 (tt0) cc_final: 0.7823 (tt0) outliers start: 21 outliers final: 17 residues processed: 166 average time/residue: 0.1631 time to fit residues: 41.9184 Evaluate side-chains 178 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 165 MET 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 436 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 543 LEU 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: 1.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 106 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10440 Z= 0.195 Angle : 0.626 11.039 14200 Z= 0.299 Chirality : 0.041 0.200 1604 Planarity : 0.004 0.054 1762 Dihedral : 3.849 17.588 1360 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.89 % Allowed : 16.16 % Favored : 81.95 % 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: 2.29 (0.17), residues: 876 sheet: -0.47 (0.81), residues: 46 loop : -1.78 (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 90 PHE 0.020 0.001 PHE B 471 TYR 0.025 0.001 TYR B 368 ARG 0.002 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 178 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (mm) REVERT: A 521 MET cc_start: 0.8741 (tpp) cc_final: 0.8448 (tpp) REVERT: A 575 LEU cc_start: 0.9175 (tp) cc_final: 0.8698 (tp) REVERT: A 689 MET cc_start: 0.9165 (tpt) cc_final: 0.8930 (tpp) REVERT: B 387 PHE cc_start: 0.8437 (t80) cc_final: 0.8077 (t80) REVERT: B 395 PHE cc_start: 0.8835 (t80) cc_final: 0.8598 (t80) REVERT: B 521 MET cc_start: 0.8924 (tpp) cc_final: 0.8124 (mmt) REVERT: B 525 TRP cc_start: 0.8762 (m-10) cc_final: 0.8102 (m-10) REVERT: B 534 MET cc_start: 0.8509 (mtp) cc_final: 0.8285 (mtt) REVERT: B 661 LEU cc_start: 0.8781 (mt) cc_final: 0.8541 (mt) REVERT: B 677 GLU cc_start: 0.8068 (tt0) cc_final: 0.7821 (tt0) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.1620 time to fit residues: 40.6630 Evaluate side-chains 173 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 165 MET 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 436 LEU Chi-restraints excluded: chain B residue 540 MET 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: 0.3980 chunk 92 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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** B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090549 restraints weight = 19798.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093421 restraints weight = 10410.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095271 restraints weight = 7078.339| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10440 Z= 0.162 Angle : 0.618 10.961 14200 Z= 0.295 Chirality : 0.041 0.208 1604 Planarity : 0.004 0.054 1762 Dihedral : 3.785 17.726 1360 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.61 % Allowed : 16.35 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1248 helix: 2.29 (0.17), residues: 876 sheet: -0.42 (0.81), 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 0.001 0.000 HIS B 607 PHE 0.018 0.001 PHE B 471 TYR 0.026 0.001 TYR B 368 ARG 0.003 0.000 ARG B 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.43 seconds wall clock time: 34 minutes 23.84 seconds (2063.84 seconds total)