Starting phenix.real_space_refine on Wed May 8 18:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xng_38503/05_2024/8xng_38503.pdb" } resolution = 3.56 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= 0.012 sd= 0.063 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 7240 2.51 5 N 1774 2.21 5 O 1858 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 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B ARG 682": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 10922 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5461 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 646} Chain breaks: 3 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: 5461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5461 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 646} Chain breaks: 3 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: 6.17, per 1000 atoms: 0.56 Number of scatterers: 10922 At special positions: 0 Unit cell: (89.675, 140.315, 108.665, 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 1858 8.00 N 1774 7.00 C 7240 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: 4.58 Conformation dependent library (CDL) restraints added in 2.1 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 72.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.699A pdb=" N ILE A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.836A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.863A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 120 removed outlier: 4.536A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.739A 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 121 through 124 removed outlier: 3.721A pdb=" N ASN A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 155 through 195 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 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 329 through 338 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 398 removed outlier: 3.510A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 420 through 437 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.907A pdb=" N GLU A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.406A pdb=" N SER A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.651A pdb=" N LYS A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.611A pdb=" N LEU A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 583 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.569A 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: 4.031A 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 removed outlier: 3.982A pdb=" N ALA A 688 " --> pdb=" O PRO A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.162A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 31 removed outlier: 3.586A pdb=" N GLN B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.836A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.861A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 120 removed outlier: 4.535A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.738A 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 121 through 124 removed outlier: 3.720A pdb=" N ASN B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 155 through 195 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 314 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 329 through 338 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 398 removed outlier: 3.510A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 420 through 437 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.907A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 494 removed outlier: 4.406A pdb=" N SER B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.651A pdb=" N LYS B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.611A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 583 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.569A 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: 4.031A 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 removed outlier: 3.982A pdb=" N ALA B 688 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.162A 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 238 removed outlier: 3.628A pdb=" N ALA A 323 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 206 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 238 removed outlier: 3.629A pdb=" N ALA B 323 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 206 " --> pdb=" O ALA B 323 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2016 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: 3.31 Time building geometry restraints manager: 4.88 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: 3302 1.34 - 1.45: 1831 1.45 - 1.57: 6001 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11226 Sorted by residual: bond pdb=" CB TRP A 348 " pdb=" CG TRP A 348 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.67e+00 bond pdb=" CB TRP B 348 " pdb=" CG TRP B 348 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.66e+00 bond pdb=" CA GLU B 618 " pdb=" CB GLU B 618 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.46e-02 4.69e+03 3.79e+00 bond pdb=" CA GLU A 618 " pdb=" CB GLU A 618 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.46e-02 4.69e+03 3.72e+00 bond pdb=" CG1 ILE A 108 " pdb=" CD1 ILE A 108 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.02e+00 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.93: 248 104.93 - 112.21: 5662 112.21 - 119.49: 3728 119.49 - 126.77: 5448 126.77 - 134.06: 180 Bond angle restraints: 15266 Sorted by residual: angle pdb=" C ALA B 133 " pdb=" N LYS B 134 " pdb=" CA LYS B 134 " ideal model delta sigma weight residual 122.23 127.88 -5.65 1.48e+00 4.57e-01 1.46e+01 angle pdb=" C ALA A 133 " pdb=" N LYS A 134 " pdb=" CA LYS A 134 " ideal model delta sigma weight residual 122.23 127.83 -5.60 1.48e+00 4.57e-01 1.43e+01 angle pdb=" C ALA A 118 " pdb=" N VAL A 119 " pdb=" CA VAL A 119 " ideal model delta sigma weight residual 122.66 119.22 3.44 9.70e-01 1.06e+00 1.26e+01 angle pdb=" C ALA B 118 " pdb=" N VAL B 119 " pdb=" CA VAL B 119 " ideal model delta sigma weight residual 122.66 119.27 3.39 9.70e-01 1.06e+00 1.22e+01 angle pdb=" N PHE A 420 " pdb=" CA PHE A 420 " pdb=" C PHE A 420 " ideal model delta sigma weight residual 113.18 108.75 4.43 1.33e+00 5.65e-01 1.11e+01 ... (remaining 15261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5915 17.28 - 34.56: 585 34.56 - 51.85: 94 51.85 - 69.13: 10 69.13 - 86.41: 16 Dihedral angle restraints: 6620 sinusoidal: 2584 harmonic: 4036 Sorted by residual: dihedral pdb=" CA ILE A 152 " pdb=" C ILE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -141.32 -38.68 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual -180.00 -141.35 -38.65 0 5.00e+00 4.00e-02 5.97e+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 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 6617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1131 0.046 - 0.092: 447 0.092 - 0.137: 135 0.137 - 0.183: 11 0.183 - 0.229: 6 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL A 476 " pdb=" CA VAL A 476 " pdb=" CG1 VAL A 476 " pdb=" CG2 VAL A 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 476 " pdb=" CA VAL B 476 " pdb=" CG1 VAL B 476 " pdb=" CG2 VAL B 476 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 579 " pdb=" CB LEU A 579 " pdb=" CD1 LEU A 579 " pdb=" CD2 LEU A 579 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1727 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 348 " -0.037 2.00e-02 2.50e+03 3.73e-02 3.47e+01 pdb=" CG TRP A 348 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP A 348 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP A 348 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 348 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 348 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 348 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 348 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 348 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 348 " 0.037 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" CG TRP B 348 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP B 348 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP B 348 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 348 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 348 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 348 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 348 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 31 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 32 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.038 5.00e-02 4.00e+02 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 12431 3.25 - 3.80: 18229 3.80 - 4.35: 21566 4.35 - 4.90: 35605 Nonbonded interactions: 88190 Sorted by model distance: nonbonded pdb=" O LYS B 303 " pdb=" OG SER B 306 " model vdw 2.146 2.440 nonbonded pdb=" O LYS A 303 " pdb=" OG SER A 306 " model vdw 2.146 2.440 nonbonded pdb=" O GLN A 135 " pdb=" ND2 ASN A 138 " model vdw 2.189 2.520 nonbonded pdb=" O GLN B 135 " pdb=" ND2 ASN B 138 " model vdw 2.189 2.520 nonbonded pdb=" O PHE B 454 " pdb=" OG1 THR B 455 " model vdw 2.194 2.440 ... (remaining 88185 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: 0.900 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: 3.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.410 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.008 0.074 11226 Z= 0.493 Angle : 0.892 9.810 15266 Z= 0.484 Chirality : 0.052 0.229 1730 Planarity : 0.006 0.069 1900 Dihedral : 14.281 86.411 3996 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.58 (0.22), residues: 1350 helix: 0.08 (0.16), residues: 894 sheet: -2.64 (0.82), residues: 46 loop : -3.39 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.004 TRP A 348 HIS 0.005 0.001 HIS B 379 PHE 0.037 0.002 PHE B 224 TYR 0.030 0.003 TYR B 468 ARG 0.011 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6373 (mtt180) cc_final: 0.4964 (mtt90) REVERT: A 180 GLU cc_start: 0.7247 (tp30) cc_final: 0.6926 (tp30) REVERT: A 260 ASP cc_start: 0.8798 (m-30) cc_final: 0.8583 (m-30) REVERT: A 303 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8075 (ptmt) REVERT: A 448 MET cc_start: 0.7717 (ttm) cc_final: 0.7340 (ttm) REVERT: A 521 MET cc_start: 0.8320 (tpp) cc_final: 0.8096 (mmm) REVERT: A 589 MET cc_start: 0.8289 (tmm) cc_final: 0.8062 (tmm) REVERT: B 253 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8913 (tptt) REVERT: B 303 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8118 (ptmt) REVERT: B 589 MET cc_start: 0.8255 (tmm) cc_final: 0.7980 (tmm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2285 time to fit residues: 74.7691 Evaluate side-chains 184 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 106 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 208 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11226 Z= 0.237 Angle : 0.675 6.968 15266 Z= 0.342 Chirality : 0.045 0.175 1730 Planarity : 0.005 0.052 1900 Dihedral : 4.748 38.783 1464 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.39 % Allowed : 13.15 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.23), residues: 1350 helix: 1.05 (0.17), residues: 898 sheet: -2.85 (0.73), residues: 46 loop : -3.23 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 348 HIS 0.004 0.001 HIS B 236 PHE 0.018 0.001 PHE A 577 TYR 0.014 0.002 TYR B 155 ARG 0.005 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6346 (mtt180) cc_final: 0.4909 (mtt90) REVERT: A 171 ILE cc_start: 0.8583 (mm) cc_final: 0.8369 (mm) REVERT: A 260 ASP cc_start: 0.8790 (m-30) cc_final: 0.8541 (m-30) REVERT: A 303 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8139 (pmmt) REVERT: A 448 MET cc_start: 0.7582 (ttm) cc_final: 0.7150 (ttm) REVERT: A 589 MET cc_start: 0.8123 (tmm) cc_final: 0.7776 (tmm) REVERT: B 165 MET cc_start: 0.8209 (mmp) cc_final: 0.7982 (mmp) REVERT: B 253 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8919 (tptt) REVERT: B 314 ASN cc_start: 0.9057 (m110) cc_final: 0.8624 (p0) REVERT: B 589 MET cc_start: 0.8055 (tmm) cc_final: 0.7328 (tmm) outliers start: 16 outliers final: 11 residues processed: 219 average time/residue: 0.2120 time to fit residues: 68.3163 Evaluate side-chains 202 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 228 ASN A 257 ASN A 397 GLN B 208 ASN B 228 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11226 Z= 0.187 Angle : 0.620 6.755 15266 Z= 0.311 Chirality : 0.043 0.185 1730 Planarity : 0.005 0.045 1900 Dihedral : 4.455 39.121 1464 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.35 % Allowed : 15.68 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.10 (0.24), residues: 1350 helix: 1.53 (0.18), residues: 886 sheet: -3.16 (0.68), residues: 46 loop : -2.91 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.002 0.001 HIS B 162 PHE 0.021 0.001 PHE A 169 TYR 0.012 0.001 TYR B 261 ARG 0.003 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.8784 (m-30) cc_final: 0.8520 (m-30) REVERT: A 448 MET cc_start: 0.7501 (ttm) cc_final: 0.7205 (ttm) REVERT: A 589 MET cc_start: 0.8055 (tmm) cc_final: 0.7176 (tmm) REVERT: B 253 LYS cc_start: 0.9236 (tmtt) cc_final: 0.8962 (tptt) REVERT: B 263 GLN cc_start: 0.9246 (tp-100) cc_final: 0.8929 (tm-30) REVERT: B 589 MET cc_start: 0.7819 (tmm) cc_final: 0.6903 (tmm) outliers start: 27 outliers final: 16 residues processed: 236 average time/residue: 0.2055 time to fit residues: 71.1774 Evaluate side-chains 207 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 578 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 208 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11226 Z= 0.174 Angle : 0.624 7.089 15266 Z= 0.309 Chirality : 0.043 0.194 1730 Planarity : 0.005 0.044 1900 Dihedral : 4.313 38.722 1464 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.44 % Allowed : 19.95 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.30 (0.24), residues: 1350 helix: 1.69 (0.18), residues: 886 sheet: -3.27 (0.68), residues: 46 loop : -2.84 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 348 HIS 0.002 0.000 HIS B 162 PHE 0.025 0.001 PHE B 169 TYR 0.021 0.001 TYR B 683 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 MET cc_start: 0.7570 (ttm) cc_final: 0.7176 (ttm) REVERT: A 521 MET cc_start: 0.7782 (mmt) cc_final: 0.7480 (mmp) REVERT: A 589 MET cc_start: 0.7866 (tmm) cc_final: 0.6980 (tmm) REVERT: A 682 ARG cc_start: 0.8925 (ptt90) cc_final: 0.8579 (ptp90) REVERT: B 165 MET cc_start: 0.8107 (mmp) cc_final: 0.7817 (tpp) REVERT: B 253 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8997 (tptp) REVERT: B 263 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8937 (tm-30) REVERT: B 307 LYS cc_start: 0.9221 (mppt) cc_final: 0.8945 (mttt) REVERT: B 589 MET cc_start: 0.7746 (tmm) cc_final: 0.6752 (tmm) outliers start: 28 outliers final: 15 residues processed: 231 average time/residue: 0.2139 time to fit residues: 72.8768 Evaluate side-chains 209 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11226 Z= 0.203 Angle : 0.626 6.844 15266 Z= 0.312 Chirality : 0.043 0.184 1730 Planarity : 0.005 0.051 1900 Dihedral : 4.283 38.968 1464 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.14 % Allowed : 21.60 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.34 (0.24), residues: 1350 helix: 1.73 (0.18), residues: 886 sheet: -3.21 (0.68), residues: 46 loop : -2.83 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 348 HIS 0.002 0.000 HIS A 714 PHE 0.033 0.001 PHE A 72 TYR 0.023 0.001 TYR A 261 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7042 (tp30) cc_final: 0.6601 (tp30) REVERT: A 184 ILE cc_start: 0.7713 (mm) cc_final: 0.7430 (mm) REVERT: A 307 LYS cc_start: 0.9201 (mppt) cc_final: 0.8973 (mtmt) REVERT: A 448 MET cc_start: 0.7566 (ttm) cc_final: 0.7196 (ttm) REVERT: A 589 MET cc_start: 0.7851 (tmm) cc_final: 0.6944 (tmm) REVERT: A 682 ARG cc_start: 0.8918 (ptt90) cc_final: 0.8537 (ptp90) REVERT: B 165 MET cc_start: 0.8115 (mmp) cc_final: 0.7857 (tpp) REVERT: B 253 LYS cc_start: 0.9280 (tmtt) cc_final: 0.8998 (tptp) REVERT: B 263 GLN cc_start: 0.9265 (tp-100) cc_final: 0.8972 (tm-30) REVERT: B 303 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8218 (ptpp) REVERT: B 307 LYS cc_start: 0.9260 (mppt) cc_final: 0.8983 (mttt) REVERT: B 366 ILE cc_start: 0.8463 (mm) cc_final: 0.8248 (mt) REVERT: B 536 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7845 (pttt) REVERT: B 589 MET cc_start: 0.7765 (tmm) cc_final: 0.6727 (tmm) outliers start: 36 outliers final: 23 residues processed: 229 average time/residue: 0.2192 time to fit residues: 73.8624 Evaluate side-chains 222 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR 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: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 208 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11226 Z= 0.169 Angle : 0.622 8.878 15266 Z= 0.305 Chirality : 0.042 0.185 1730 Planarity : 0.004 0.044 1900 Dihedral : 4.199 38.997 1464 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.61 % Allowed : 22.82 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.51 (0.24), residues: 1350 helix: 1.83 (0.18), residues: 888 sheet: -3.24 (0.66), residues: 46 loop : -2.69 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 348 HIS 0.002 0.000 HIS B 628 PHE 0.033 0.001 PHE A 72 TYR 0.025 0.001 TYR A 261 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 165 MET cc_start: 0.8459 (tpp) cc_final: 0.8233 (tpp) REVERT: A 307 LYS cc_start: 0.9197 (mppt) cc_final: 0.8961 (mtmt) REVERT: A 448 MET cc_start: 0.7539 (ttm) cc_final: 0.7191 (ttm) REVERT: A 589 MET cc_start: 0.7715 (tmm) cc_final: 0.6771 (tmm) REVERT: A 682 ARG cc_start: 0.8846 (ptt90) cc_final: 0.8552 (ptp90) REVERT: B 253 LYS cc_start: 0.9269 (tmtt) cc_final: 0.8989 (tptp) REVERT: B 263 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8969 (tm-30) REVERT: B 303 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8291 (ptpp) REVERT: B 307 LYS cc_start: 0.9263 (mppt) cc_final: 0.8978 (mttt) REVERT: B 536 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7865 (pttt) REVERT: B 589 MET cc_start: 0.7700 (tmm) cc_final: 0.6722 (tmm) outliers start: 30 outliers final: 22 residues processed: 230 average time/residue: 0.2222 time to fit residues: 74.4440 Evaluate side-chains 221 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL 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: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 0.0040 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 208 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11226 Z= 0.165 Angle : 0.625 8.456 15266 Z= 0.308 Chirality : 0.042 0.186 1730 Planarity : 0.004 0.052 1900 Dihedral : 4.148 39.011 1464 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.53 % Allowed : 23.87 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.40 (0.24), residues: 1350 helix: 1.75 (0.18), residues: 900 sheet: -3.35 (0.61), residues: 50 loop : -2.88 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 348 HIS 0.002 0.000 HIS A 229 PHE 0.035 0.001 PHE A 72 TYR 0.026 0.001 TYR A 261 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.5985 (mtt180) cc_final: 0.4609 (mtt90) REVERT: A 157 MET cc_start: 0.5680 (mpp) cc_final: 0.5419 (mpp) REVERT: A 165 MET cc_start: 0.8437 (tpp) cc_final: 0.8229 (tpp) REVERT: A 307 LYS cc_start: 0.9205 (mppt) cc_final: 0.8978 (mtmt) REVERT: A 448 MET cc_start: 0.7479 (ttm) cc_final: 0.7125 (ttm) REVERT: A 589 MET cc_start: 0.7582 (tmm) cc_final: 0.6620 (tmm) REVERT: A 682 ARG cc_start: 0.8807 (ptt90) cc_final: 0.8542 (ptp90) REVERT: B 165 MET cc_start: 0.8234 (mmp) cc_final: 0.7993 (tpp) REVERT: B 263 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8973 (tm-30) REVERT: B 307 LYS cc_start: 0.9253 (mppt) cc_final: 0.8946 (mtmt) REVERT: B 511 MET cc_start: 0.6367 (pmm) cc_final: 0.6142 (pmm) REVERT: B 589 MET cc_start: 0.7616 (tmm) cc_final: 0.6581 (tmm) outliers start: 29 outliers final: 24 residues processed: 227 average time/residue: 0.2065 time to fit residues: 68.7919 Evaluate side-chains 220 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11226 Z= 0.272 Angle : 0.681 9.326 15266 Z= 0.340 Chirality : 0.045 0.212 1730 Planarity : 0.005 0.050 1900 Dihedral : 4.290 39.450 1464 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.22 % Allowed : 24.13 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.16 (0.24), residues: 1350 helix: 1.50 (0.17), residues: 910 sheet: -3.10 (0.65), residues: 46 loop : -2.96 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 348 HIS 0.004 0.001 HIS A 714 PHE 0.037 0.002 PHE A 72 TYR 0.029 0.002 TYR B 261 ARG 0.002 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.5817 (mtt180) cc_final: 0.4444 (mtt90) REVERT: A 165 MET cc_start: 0.8468 (tpp) cc_final: 0.8212 (tpp) REVERT: A 307 LYS cc_start: 0.9191 (mppt) cc_final: 0.8971 (mtmt) REVERT: A 448 MET cc_start: 0.7497 (ttm) cc_final: 0.7056 (ttm) REVERT: A 511 MET cc_start: 0.6445 (pmm) cc_final: 0.6220 (pmm) REVERT: A 589 MET cc_start: 0.7723 (tmm) cc_final: 0.7170 (tmm) REVERT: A 682 ARG cc_start: 0.8855 (ptt90) cc_final: 0.8571 (ptp90) REVERT: B 165 MET cc_start: 0.8156 (mmp) cc_final: 0.7950 (tpp) REVERT: B 263 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8975 (tm-30) REVERT: B 307 LYS cc_start: 0.9238 (mppt) cc_final: 0.8932 (mtmt) REVERT: B 511 MET cc_start: 0.6420 (pmm) cc_final: 0.6189 (pmm) REVERT: B 589 MET cc_start: 0.7844 (tmm) cc_final: 0.6809 (tmm) outliers start: 37 outliers final: 29 residues processed: 223 average time/residue: 0.2077 time to fit residues: 67.9717 Evaluate side-chains 222 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 129 optimal weight: 0.0570 overall best weight: 1.3104 ------------------------------------------------------------------------------- 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 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 257 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11226 Z= 0.194 Angle : 0.659 8.875 15266 Z= 0.323 Chirality : 0.043 0.194 1730 Planarity : 0.004 0.044 1900 Dihedral : 4.214 39.104 1464 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.79 % Allowed : 25.52 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.30 (0.24), residues: 1350 helix: 1.63 (0.18), residues: 902 sheet: -3.01 (0.65), residues: 46 loop : -2.90 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 348 HIS 0.002 0.000 HIS B 236 PHE 0.036 0.001 PHE A 72 TYR 0.027 0.001 TYR B 261 ARG 0.003 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.5664 (mtt180) cc_final: 0.4352 (mtt90) REVERT: A 180 GLU cc_start: 0.7242 (tp30) cc_final: 0.7019 (tp30) REVERT: A 307 LYS cc_start: 0.9175 (mppt) cc_final: 0.8959 (mtmt) REVERT: A 448 MET cc_start: 0.7483 (ttm) cc_final: 0.7037 (ttm) REVERT: A 469 TYR cc_start: 0.8860 (t80) cc_final: 0.8634 (t80) REVERT: A 511 MET cc_start: 0.6266 (pmm) cc_final: 0.6040 (pmm) REVERT: A 589 MET cc_start: 0.7780 (tmm) cc_final: 0.6910 (tmm) REVERT: A 682 ARG cc_start: 0.8775 (ptt90) cc_final: 0.8493 (ptp90) REVERT: B 257 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8764 (m110) REVERT: B 263 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8980 (tm-30) REVERT: B 307 LYS cc_start: 0.9257 (mppt) cc_final: 0.8949 (mtmt) REVERT: B 511 MET cc_start: 0.6326 (pmm) cc_final: 0.6091 (pmm) REVERT: B 589 MET cc_start: 0.7884 (tmm) cc_final: 0.7410 (ttp) outliers start: 32 outliers final: 25 residues processed: 225 average time/residue: 0.1950 time to fit residues: 65.0287 Evaluate side-chains 223 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 256 GLN B 257 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11226 Z= 0.171 Angle : 0.681 12.537 15266 Z= 0.326 Chirality : 0.043 0.201 1730 Planarity : 0.004 0.041 1900 Dihedral : 4.200 39.157 1464 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.26 % Allowed : 26.13 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.35 (0.24), residues: 1350 helix: 1.66 (0.18), residues: 902 sheet: -2.99 (0.64), residues: 46 loop : -2.84 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 348 HIS 0.002 0.000 HIS B 628 PHE 0.037 0.001 PHE A 72 TYR 0.029 0.001 TYR A 261 ARG 0.004 0.000 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.5594 (mtt180) cc_final: 0.4278 (mtt90) REVERT: A 266 TYR cc_start: 0.8069 (t80) cc_final: 0.7703 (t80) REVERT: A 307 LYS cc_start: 0.9168 (mppt) cc_final: 0.8939 (mtmt) REVERT: A 448 MET cc_start: 0.7566 (ttm) cc_final: 0.7176 (ttm) REVERT: A 511 MET cc_start: 0.6258 (pmm) cc_final: 0.6020 (pmm) REVERT: A 589 MET cc_start: 0.7679 (tmm) cc_final: 0.6846 (tmm) REVERT: B 263 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8982 (tm-30) REVERT: B 307 LYS cc_start: 0.9252 (mppt) cc_final: 0.8939 (mtmt) REVERT: B 511 MET cc_start: 0.6336 (pmm) cc_final: 0.6085 (pmm) REVERT: B 589 MET cc_start: 0.7812 (tmm) cc_final: 0.7398 (ttp) outliers start: 26 outliers final: 23 residues processed: 231 average time/residue: 0.2214 time to fit residues: 73.9996 Evaluate side-chains 222 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.139528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113147 restraints weight = 23914.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115974 restraints weight = 12094.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117566 restraints weight = 7850.455| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11226 Z= 0.195 Angle : 0.685 10.055 15266 Z= 0.334 Chirality : 0.043 0.254 1730 Planarity : 0.004 0.039 1900 Dihedral : 4.191 39.110 1464 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.18 % Allowed : 26.22 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.33 (0.24), residues: 1350 helix: 1.60 (0.18), residues: 910 sheet: -2.85 (0.65), residues: 46 loop : -2.86 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 348 HIS 0.002 0.000 HIS A 542 PHE 0.037 0.001 PHE A 72 TYR 0.029 0.001 TYR A 261 ARG 0.006 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.91 seconds wall clock time: 41 minutes 39.08 seconds (2499.08 seconds total)