Starting phenix.real_space_refine on Sun Aug 4 17:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs4_38614/08_2024/8xs4_38614.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.093 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 50 5.16 5 C 7366 2.51 5 N 1814 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 699": "OE1" <-> "OE2" 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: 11132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5566 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 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: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5566 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 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: 6.39, per 1000 atoms: 0.57 Number of scatterers: 11132 At special positions: 0 Unit cell: (87.565, 145.59, 101.28, 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 50 16.00 O 1902 8.00 N 1814 7.00 C 7366 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: 4.48 Conformation dependent library (CDL) restraints added in 2.1 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 2 sheets defined 69.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.536A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 39' Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.121A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 120 removed outlier: 3.678A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (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 216 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 289 through 314 removed outlier: 3.711A pdb=" N ASN A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' 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 removed outlier: 3.541A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.521A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.728A pdb=" N ALA A 408 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 504 through 532 Proline residue: A 510 - end of helix removed outlier: 3.882A pdb=" N THR A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.991A pdb=" N VAL A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 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: 3.548A 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: 4.119A 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 709 Processing helix chain 'B' and resid 4 through 31 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.536A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 39' Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.121A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 120 removed outlier: 3.679A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (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 216 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 289 through 314 removed outlier: 3.711A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' 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 removed outlier: 3.542A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.522A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.729A pdb=" N ALA B 408 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 504 through 532 Proline residue: B 510 - end of helix removed outlier: 3.882A pdb=" N THR B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 removed outlier: 3.990A pdb=" N VAL B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 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: 3.548A 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: 4.119A 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 709 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.447A 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: 5.448A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2043 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: 3.33 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3426 1.34 - 1.46: 2762 1.46 - 1.58: 5164 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 11444 Sorted by residual: bond pdb=" CG GLU B 452 " pdb=" CD GLU B 452 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.13e+00 bond pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.07e+00 bond pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.62e-02 3.81e+03 1.12e+00 bond pdb=" CB PRO A 392 " pdb=" CG PRO A 392 " ideal model delta sigma weight residual 1.492 1.439 0.053 5.00e-02 4.00e+02 1.12e+00 bond pdb=" CA GLU B 452 " pdb=" CB GLU B 452 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.62e-02 3.81e+03 1.11e+00 ... (remaining 11439 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.58: 371 106.58 - 113.45: 6214 113.45 - 120.33: 4429 120.33 - 127.21: 4413 127.21 - 134.09: 149 Bond angle restraints: 15576 Sorted by residual: angle pdb=" C PHE A 454 " pdb=" N THR A 455 " pdb=" CA THR A 455 " ideal model delta sigma weight residual 122.08 127.12 -5.04 1.47e+00 4.63e-01 1.18e+01 angle pdb=" C PHE B 454 " pdb=" N THR B 455 " pdb=" CA THR B 455 " ideal model delta sigma weight residual 122.08 127.10 -5.02 1.47e+00 4.63e-01 1.17e+01 angle pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " ideal model delta sigma weight residual 114.10 107.74 6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLU B 452 " pdb=" CB GLU B 452 " pdb=" CG GLU B 452 " ideal model delta sigma weight residual 114.10 107.75 6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA LEU B 73 " pdb=" CB LEU B 73 " pdb=" CG LEU B 73 " ideal model delta sigma weight residual 116.30 127.25 -10.95 3.50e+00 8.16e-02 9.80e+00 ... (remaining 15571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6086 17.41 - 34.81: 538 34.81 - 52.22: 100 52.22 - 69.62: 8 69.62 - 87.03: 16 Dihedral angle restraints: 6748 sinusoidal: 2630 harmonic: 4118 Sorted by residual: dihedral pdb=" CA VAL A 119 " pdb=" C VAL A 119 " pdb=" N LEU A 120 " pdb=" CA LEU A 120 " ideal model delta harmonic sigma weight residual -180.00 -155.99 -24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL B 119 " pdb=" C VAL B 119 " pdb=" N LEU B 120 " pdb=" CA LEU B 120 " ideal model delta harmonic sigma weight residual 180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LYS B 413 " pdb=" C LYS B 413 " pdb=" N PHE B 414 " pdb=" CA PHE B 414 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1244 0.043 - 0.087: 388 0.087 - 0.130: 113 0.130 - 0.174: 15 0.174 - 0.217: 4 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1761 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 76 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 77 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 76 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 77 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.022 2.00e-02 2.50e+03 1.83e-02 6.73e+00 pdb=" CG TYR A 181 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " 0.002 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 262 2.70 - 3.25: 11490 3.25 - 3.80: 17976 3.80 - 4.35: 22645 4.35 - 4.90: 38125 Nonbonded interactions: 90498 Sorted by model distance: nonbonded pdb=" OE1 GLU B 222 " pdb=" OH TYR B 233 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLU A 222 " pdb=" OH TYR A 233 " model vdw 2.149 3.040 nonbonded pdb=" NH1 ARG A 374 " pdb=" O PHE A 451 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG B 374 " pdb=" O PHE B 451 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP A 143 " pdb=" OG1 THR A 514 " model vdw 2.235 3.040 ... (remaining 90493 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.040 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.004 0.053 11444 Z= 0.256 Angle : 0.797 10.954 15576 Z= 0.424 Chirality : 0.046 0.217 1764 Planarity : 0.006 0.065 1946 Dihedral : 13.899 87.027 4072 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.41 (0.24), residues: 1384 helix: 1.14 (0.18), residues: 882 sheet: -2.18 (0.85), residues: 42 loop : -3.03 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 75 HIS 0.003 0.001 HIS B 628 PHE 0.036 0.002 PHE A 33 TYR 0.045 0.002 TYR A 181 ARG 0.004 0.001 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.259 Fit side-chains REVERT: A 98 TYR cc_start: 0.8736 (t80) cc_final: 0.8492 (t80) REVERT: A 117 TRP cc_start: 0.7700 (m100) cc_final: 0.7478 (m100) REVERT: A 422 LYS cc_start: 0.7426 (mmtt) cc_final: 0.7132 (mmtt) REVERT: A 521 MET cc_start: 0.7883 (mtm) cc_final: 0.7471 (mtp) REVERT: A 547 PHE cc_start: 0.8080 (m-10) cc_final: 0.7833 (m-10) REVERT: A 613 TYR cc_start: 0.7996 (m-10) cc_final: 0.7640 (m-10) REVERT: B 395 PHE cc_start: 0.9086 (t80) cc_final: 0.8886 (t80) REVERT: B 422 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7278 (mmtt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1887 time to fit residues: 55.6741 Evaluate side-chains 164 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 615 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.053 11444 Z= 0.209 Angle : 0.686 10.336 15576 Z= 0.338 Chirality : 0.043 0.203 1764 Planarity : 0.006 0.060 1946 Dihedral : 5.022 20.751 1494 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.85 % Allowed : 7.85 % Favored : 91.30 % 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: 0.01 (0.24), residues: 1384 helix: 1.46 (0.18), residues: 888 sheet: -2.54 (0.76), residues: 42 loop : -2.83 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS B 90 PHE 0.028 0.001 PHE B 33 TYR 0.025 0.001 TYR B 181 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.003 Fit side-chains REVERT: A 98 TYR cc_start: 0.8684 (t80) cc_final: 0.8359 (t80) REVERT: A 422 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7208 (mmtt) REVERT: A 613 TYR cc_start: 0.7973 (m-10) cc_final: 0.7654 (m-10) REVERT: B 395 PHE cc_start: 0.9144 (t80) cc_final: 0.8926 (t80) REVERT: B 422 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7069 (mmtt) REVERT: B 583 TYR cc_start: 0.7504 (m-80) cc_final: 0.7246 (m-10) outliers start: 10 outliers final: 7 residues processed: 173 average time/residue: 0.1827 time to fit residues: 48.3080 Evaluate side-chains 166 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.0570 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 125 optimal weight: 0.1980 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11444 Z= 0.188 Angle : 0.638 9.914 15576 Z= 0.315 Chirality : 0.043 0.187 1764 Planarity : 0.006 0.058 1946 Dihedral : 4.743 19.225 1494 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.54 % Allowed : 11.86 % Favored : 86.60 % 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: 0.29 (0.24), residues: 1384 helix: 1.65 (0.18), residues: 894 sheet: -2.94 (0.69), residues: 42 loop : -2.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.025 0.001 PHE B 33 TYR 0.019 0.001 TYR B 181 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.193 Fit side-chains REVERT: A 422 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7186 (mmtt) REVERT: A 613 TYR cc_start: 0.8001 (m-10) cc_final: 0.7755 (m-10) REVERT: B 422 LYS cc_start: 0.7399 (mmtt) cc_final: 0.7162 (mmtt) REVERT: B 578 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7386 (tt) outliers start: 18 outliers final: 6 residues processed: 174 average time/residue: 0.1939 time to fit residues: 50.9679 Evaluate side-chains 160 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 65 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11444 Z= 0.218 Angle : 0.628 10.119 15576 Z= 0.309 Chirality : 0.043 0.177 1764 Planarity : 0.005 0.059 1946 Dihedral : 4.599 18.821 1494 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.71 % Allowed : 13.65 % Favored : 84.64 % 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: 0.48 (0.24), residues: 1384 helix: 1.80 (0.18), residues: 884 sheet: -3.09 (0.67), residues: 42 loop : -2.44 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.022 0.001 PHE B 33 TYR 0.021 0.001 TYR A 181 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.671 Fit side-chains REVERT: A 257 ASN cc_start: 0.8471 (m110) cc_final: 0.8241 (m110) REVERT: A 422 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7177 (mmtt) REVERT: A 531 GLU cc_start: 0.7234 (tp30) cc_final: 0.6619 (mm-30) REVERT: A 613 TYR cc_start: 0.8052 (m-10) cc_final: 0.7804 (m-10) REVERT: B 531 GLU cc_start: 0.7350 (tp30) cc_final: 0.6940 (mm-30) REVERT: B 578 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7449 (tt) outliers start: 20 outliers final: 10 residues processed: 176 average time/residue: 0.1705 time to fit residues: 46.7385 Evaluate side-chains 170 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11444 Z= 0.220 Angle : 0.626 9.779 15576 Z= 0.309 Chirality : 0.043 0.167 1764 Planarity : 0.005 0.058 1946 Dihedral : 4.563 20.032 1494 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.62 % Allowed : 15.53 % Favored : 82.85 % 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: 0.59 (0.24), residues: 1384 helix: 1.88 (0.18), residues: 884 sheet: -3.11 (0.66), residues: 42 loop : -2.39 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.023 0.001 PHE A 383 TYR 0.017 0.001 TYR A 181 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.148 Fit side-chains REVERT: A 82 MET cc_start: 0.7778 (ttp) cc_final: 0.7467 (ttt) REVERT: A 98 TYR cc_start: 0.8867 (t80) cc_final: 0.8501 (t80) REVERT: A 256 GLN cc_start: 0.8546 (tp40) cc_final: 0.8210 (tp40) REVERT: A 257 ASN cc_start: 0.8574 (m110) cc_final: 0.8312 (m110) REVERT: A 422 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7134 (mmtt) REVERT: A 531 GLU cc_start: 0.7231 (tp30) cc_final: 0.6672 (mm-30) REVERT: A 613 TYR cc_start: 0.8076 (m-10) cc_final: 0.7802 (m-10) REVERT: B 256 GLN cc_start: 0.8542 (tp40) cc_final: 0.8329 (tp40) REVERT: B 422 LYS cc_start: 0.7389 (mmtt) cc_final: 0.7125 (mmtt) REVERT: B 531 GLU cc_start: 0.7278 (tp30) cc_final: 0.6854 (mm-30) REVERT: B 578 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7483 (tt) outliers start: 19 outliers final: 9 residues processed: 168 average time/residue: 0.1779 time to fit residues: 46.1824 Evaluate side-chains 164 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11444 Z= 0.268 Angle : 0.654 15.171 15576 Z= 0.318 Chirality : 0.044 0.207 1764 Planarity : 0.005 0.061 1946 Dihedral : 4.549 19.181 1494 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.22 % Allowed : 15.87 % Favored : 81.91 % 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: 0.56 (0.24), residues: 1384 helix: 1.88 (0.18), residues: 882 sheet: -3.35 (0.59), residues: 46 loop : -2.41 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 PHE 0.020 0.001 PHE B 33 TYR 0.020 0.001 TYR A 181 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.201 Fit side-chains REVERT: A 98 TYR cc_start: 0.8865 (t80) cc_final: 0.8609 (t80) REVERT: A 256 GLN cc_start: 0.8516 (tp40) cc_final: 0.8183 (tp40) REVERT: A 257 ASN cc_start: 0.8554 (m110) cc_final: 0.8273 (m110) REVERT: A 531 GLU cc_start: 0.7227 (tp30) cc_final: 0.6678 (mm-30) REVERT: A 613 TYR cc_start: 0.8110 (m-10) cc_final: 0.7868 (m-10) REVERT: B 4 LEU cc_start: 0.7648 (tt) cc_final: 0.7061 (tp) REVERT: B 422 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7201 (mmtt) REVERT: B 531 GLU cc_start: 0.7255 (tp30) cc_final: 0.6846 (mm-30) REVERT: B 560 ASP cc_start: 0.6813 (t0) cc_final: 0.6309 (p0) REVERT: B 578 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7451 (tt) outliers start: 26 outliers final: 14 residues processed: 169 average time/residue: 0.1743 time to fit residues: 45.6968 Evaluate side-chains 167 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11444 Z= 0.222 Angle : 0.642 13.958 15576 Z= 0.312 Chirality : 0.043 0.322 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.506 21.553 1494 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.79 % Allowed : 17.24 % Favored : 80.97 % 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: 0.65 (0.24), residues: 1384 helix: 1.93 (0.18), residues: 884 sheet: -3.26 (0.60), residues: 46 loop : -2.33 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.027 0.001 PHE A 383 TYR 0.024 0.001 TYR A 583 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.144 Fit side-chains REVERT: A 82 MET cc_start: 0.7652 (ttp) cc_final: 0.7321 (ttt) REVERT: A 98 TYR cc_start: 0.8866 (t80) cc_final: 0.8522 (t80) REVERT: A 256 GLN cc_start: 0.8490 (tp40) cc_final: 0.8148 (tp40) REVERT: A 257 ASN cc_start: 0.8533 (m110) cc_final: 0.8300 (m110) REVERT: A 422 LYS cc_start: 0.7735 (mptt) cc_final: 0.6728 (mmtt) REVERT: A 531 GLU cc_start: 0.7101 (tp30) cc_final: 0.6576 (mm-30) REVERT: A 613 TYR cc_start: 0.8087 (m-10) cc_final: 0.7840 (m-10) REVERT: B 4 LEU cc_start: 0.7590 (tt) cc_final: 0.6994 (tp) REVERT: B 256 GLN cc_start: 0.8539 (tp40) cc_final: 0.8316 (tp40) REVERT: B 531 GLU cc_start: 0.7206 (tp30) cc_final: 0.6779 (mm-30) REVERT: B 578 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7450 (tt) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 0.1845 time to fit residues: 47.9279 Evaluate side-chains 162 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11444 Z= 0.243 Angle : 0.665 13.905 15576 Z= 0.319 Chirality : 0.044 0.399 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.491 20.620 1494 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.13 % Allowed : 16.72 % Favored : 81.14 % 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: 0.59 (0.24), residues: 1384 helix: 1.87 (0.18), residues: 888 sheet: -3.30 (0.59), residues: 46 loop : -2.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.019 0.001 PHE B 33 TYR 0.015 0.001 TYR A 583 ARG 0.003 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.200 Fit side-chains REVERT: A 98 TYR cc_start: 0.8850 (t80) cc_final: 0.8569 (t80) REVERT: A 256 GLN cc_start: 0.8495 (tp40) cc_final: 0.8204 (tp40) REVERT: A 257 ASN cc_start: 0.8546 (m110) cc_final: 0.8314 (m110) REVERT: A 422 LYS cc_start: 0.7741 (mptt) cc_final: 0.7307 (mmtt) REVERT: A 531 GLU cc_start: 0.7019 (tp30) cc_final: 0.6528 (mm-30) REVERT: A 613 TYR cc_start: 0.8104 (m-10) cc_final: 0.7848 (m-10) REVERT: B 4 LEU cc_start: 0.7545 (tt) cc_final: 0.6975 (tp) REVERT: B 256 GLN cc_start: 0.8540 (tp40) cc_final: 0.8289 (tp40) REVERT: B 422 LYS cc_start: 0.7391 (mmtt) cc_final: 0.7191 (mmtt) REVERT: B 531 GLU cc_start: 0.7199 (tp30) cc_final: 0.6772 (mm-30) REVERT: B 578 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7444 (tt) outliers start: 25 outliers final: 16 residues processed: 171 average time/residue: 0.1853 time to fit residues: 48.4807 Evaluate side-chains 167 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.7980 chunk 116 optimal weight: 30.0000 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11444 Z= 0.225 Angle : 0.676 16.704 15576 Z= 0.320 Chirality : 0.044 0.278 1764 Planarity : 0.005 0.062 1946 Dihedral : 4.491 21.632 1494 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.54 % Allowed : 17.58 % Favored : 80.89 % 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: 0.61 (0.24), residues: 1384 helix: 1.88 (0.18), residues: 888 sheet: -3.24 (0.60), residues: 46 loop : -2.34 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.028 0.001 PHE A 383 TYR 0.015 0.001 TYR A 43 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.192 Fit side-chains REVERT: A 48 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7733 (ttt180) REVERT: A 256 GLN cc_start: 0.8486 (tp40) cc_final: 0.8188 (tp40) REVERT: A 257 ASN cc_start: 0.8546 (m110) cc_final: 0.8317 (m110) REVERT: A 422 LYS cc_start: 0.7793 (mptt) cc_final: 0.7341 (mmtt) REVERT: A 531 GLU cc_start: 0.7008 (tp30) cc_final: 0.6484 (mm-30) REVERT: A 613 TYR cc_start: 0.8104 (m-10) cc_final: 0.7847 (m-10) REVERT: B 4 LEU cc_start: 0.7642 (tt) cc_final: 0.7055 (tp) REVERT: B 256 GLN cc_start: 0.8515 (tp40) cc_final: 0.8133 (tp40) REVERT: B 422 LYS cc_start: 0.7363 (mmtt) cc_final: 0.7072 (mmtt) REVERT: B 531 GLU cc_start: 0.7188 (tp30) cc_final: 0.6682 (mm-30) REVERT: B 578 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7318 (tt) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 0.1810 time to fit residues: 45.1413 Evaluate side-chains 161 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.0370 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 0.0020 chunk 116 optimal weight: 10.0000 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11444 Z= 0.179 Angle : 0.668 15.516 15576 Z= 0.313 Chirality : 0.042 0.229 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.393 20.697 1494 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.02 % Allowed : 17.83 % Favored : 81.14 % 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: 0.77 (0.24), residues: 1384 helix: 1.98 (0.18), residues: 884 sheet: -2.31 (0.80), residues: 34 loop : -2.30 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.004 0.001 HIS B 628 PHE 0.019 0.001 PHE B 33 TYR 0.013 0.001 TYR A 583 ARG 0.001 0.000 ARG B 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.224 Fit side-chains REVERT: A 256 GLN cc_start: 0.8483 (tp40) cc_final: 0.8237 (tp40) REVERT: A 257 ASN cc_start: 0.8543 (m110) cc_final: 0.8339 (m110) REVERT: A 422 LYS cc_start: 0.7809 (mptt) cc_final: 0.7341 (mmtt) REVERT: A 531 GLU cc_start: 0.6895 (tp30) cc_final: 0.6437 (mm-30) REVERT: B 4 LEU cc_start: 0.7613 (tt) cc_final: 0.7019 (tp) REVERT: B 422 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6952 (mmtt) REVERT: B 446 MET cc_start: 0.8156 (tpp) cc_final: 0.7955 (tpt) REVERT: B 511 MET cc_start: 0.7307 (mpp) cc_final: 0.7093 (mpp) REVERT: B 531 GLU cc_start: 0.6977 (tp30) cc_final: 0.6526 (mm-30) outliers start: 12 outliers final: 9 residues processed: 161 average time/residue: 0.1831 time to fit residues: 45.9765 Evaluate side-chains 162 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN B 340 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.188980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136491 restraints weight = 12502.253| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.94 r_work: 0.3074 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11444 Z= 0.234 Angle : 0.683 20.546 15576 Z= 0.323 Chirality : 0.043 0.261 1764 Planarity : 0.005 0.061 1946 Dihedral : 4.393 21.100 1494 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.02 % Allowed : 17.92 % Favored : 81.06 % 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: 0.65 (0.24), residues: 1384 helix: 1.91 (0.18), residues: 888 sheet: -3.14 (0.61), residues: 46 loop : -2.35 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.024 0.001 PHE A 383 TYR 0.015 0.001 TYR A 181 ARG 0.002 0.000 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.02 seconds wall clock time: 40 minutes 21.93 seconds (2421.93 seconds total)