Starting phenix.real_space_refine on Sun Apr 7 16:23:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/04_2024/7lgm_23327_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 46 5.16 5 C 6842 2.51 5 N 1942 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5446 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 25, 'TRANS': 693} Chain: "B" Number of atoms: 5446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5446 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 25, 'TRANS': 693} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.97, per 1000 atoms: 0.55 Number of scatterers: 10954 At special positions: 0 Unit cell: (121.8, 138.04, 97.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 6 15.00 O 2118 8.00 N 1942 7.00 C 6842 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: 4.31 Conformation dependent library (CDL) restraints added in 2.4 seconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 16 sheets defined 31.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.624A pdb=" N ASN A 45 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 164 through 176 removed outlier: 4.135A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.535A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.010A pdb=" N ASP A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.697A pdb=" N GLN A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 368 Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.938A pdb=" N MET A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.879A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 646 through 648 No H-bonds generated for 'chain 'A' and resid 646 through 648' Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing helix chain 'A' and resid 693 through 705 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.624A pdb=" N ASN B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 76 through 83 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.135A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.535A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.010A pdb=" N ASP B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.697A pdb=" N GLN B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 368 Processing helix chain 'B' and resid 406 through 419 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.938A pdb=" N MET B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 509 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 594 through 604 removed outlier: 3.879A pdb=" N VAL B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 682 through 684 No H-bonds generated for 'chain 'B' and resid 682 through 684' Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 711 through 718 Processing sheet with id= A, first strand: chain 'A' and resid 107 through 112 removed outlier: 6.089A pdb=" N VAL A 24 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 3 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 Processing sheet with id= D, first strand: chain 'A' and resid 424 through 430 Processing sheet with id= E, first strand: chain 'A' and resid 323 through 325 Processing sheet with id= F, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.654A pdb=" N VAL A 572 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR A 608 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL A 575 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 610 " --> pdb=" O VAL A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 632 through 634 removed outlier: 6.221A pdb=" N ILE A 666 " --> pdb=" O PRO A 674 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU A 668 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.917A pdb=" N ILE A 550 " --> pdb=" O GLY A 514 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.089A pdb=" N VAL B 24 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE B 3 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 180 through 182 Processing sheet with id= K, first strand: chain 'B' and resid 256 through 260 Processing sheet with id= L, first strand: chain 'B' and resid 424 through 430 Processing sheet with id= M, first strand: chain 'B' and resid 323 through 325 Processing sheet with id= N, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.653A pdb=" N VAL B 572 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR B 608 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 575 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 610 " --> pdb=" O VAL B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 632 through 634 removed outlier: 6.222A pdb=" N ILE B 666 " --> pdb=" O PRO B 674 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU B 668 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.916A pdb=" N ILE B 550 " --> pdb=" O GLY B 514 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 320 hydrogen bonds defined for protein. 870 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: 3.49 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1989 1.31 - 1.44: 2642 1.44 - 1.57: 6293 1.57 - 1.70: 112 1.70 - 1.83: 80 Bond restraints: 11116 Sorted by residual: bond pdb=" CB HIS A 645 " pdb=" CG HIS A 645 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" CB HIS B 645 " pdb=" CG HIS B 645 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.28e+01 bond pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 1.512 1.395 0.117 2.20e-02 2.07e+03 2.85e+01 bond pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 1.512 1.395 0.117 2.20e-02 2.07e+03 2.80e+01 bond pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 11111 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.17: 292 105.17 - 112.33: 5202 112.33 - 119.50: 4373 119.50 - 126.67: 5086 126.67 - 133.83: 129 Bond angle restraints: 15082 Sorted by residual: angle pdb=" N LEU B 591 " pdb=" CA LEU B 591 " pdb=" C LEU B 591 " ideal model delta sigma weight residual 113.88 99.86 14.02 1.23e+00 6.61e-01 1.30e+02 angle pdb=" N LEU A 591 " pdb=" CA LEU A 591 " pdb=" C LEU A 591 " ideal model delta sigma weight residual 113.88 99.87 14.01 1.23e+00 6.61e-01 1.30e+02 angle pdb=" CA ASP A 662 " pdb=" CB ASP A 662 " pdb=" CG ASP A 662 " ideal model delta sigma weight residual 112.60 121.57 -8.97 1.00e+00 1.00e+00 8.04e+01 angle pdb=" CA ASP B 662 " pdb=" CB ASP B 662 " pdb=" CG ASP B 662 " ideal model delta sigma weight residual 112.60 121.51 -8.91 1.00e+00 1.00e+00 7.94e+01 angle pdb=" N THR A 52 " pdb=" CA THR A 52 " pdb=" C THR A 52 " ideal model delta sigma weight residual 114.56 104.13 10.43 1.27e+00 6.20e-01 6.75e+01 ... (remaining 15077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6485 17.54 - 35.08: 214 35.08 - 52.62: 49 52.62 - 70.16: 26 70.16 - 87.70: 4 Dihedral angle restraints: 6778 sinusoidal: 2694 harmonic: 4084 Sorted by residual: dihedral pdb=" C TRP A 677 " pdb=" N TRP A 677 " pdb=" CA TRP A 677 " pdb=" CB TRP A 677 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N PHE B 254 " pdb=" C PHE B 254 " pdb=" CA PHE B 254 " pdb=" CB PHE B 254 " ideal model delta harmonic sigma weight residual 122.80 131.80 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TRP B 677 " pdb=" N TRP B 677 " pdb=" CA TRP B 677 " pdb=" CB TRP B 677 " ideal model delta harmonic sigma weight residual -122.60 -113.61 -8.99 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 6775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1197 0.097 - 0.193: 465 0.193 - 0.290: 96 0.290 - 0.387: 8 0.387 - 0.484: 2 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA PHE A 254 " pdb=" N PHE A 254 " pdb=" C PHE A 254 " pdb=" CB PHE A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA PHE B 254 " pdb=" N PHE B 254 " pdb=" C PHE B 254 " pdb=" CB PHE B 254 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA SER A 209 " pdb=" N SER A 209 " pdb=" C SER A 209 " pdb=" CB SER A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1765 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 196 " 0.055 2.00e-02 2.50e+03 2.92e-02 1.71e+01 pdb=" CG TYR A 196 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 196 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 196 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 196 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 196 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 196 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 196 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 196 " -0.055 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 196 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 196 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 196 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 196 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 196 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 196 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 196 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " 0.047 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.040 2.00e-02 2.50e+03 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4459 2.90 - 3.40: 10999 3.40 - 3.90: 18708 3.90 - 4.40: 22286 4.40 - 4.90: 34210 Nonbonded interactions: 90662 Sorted by model distance: nonbonded pdb=" N LEU B 591 " pdb=" N ASP B 592 " model vdw 2.398 2.560 nonbonded pdb=" N LEU A 591 " pdb=" N ASP A 592 " model vdw 2.398 2.560 nonbonded pdb=" N ASP A 145 " pdb=" OD1 ASP A 145 " model vdw 2.425 2.520 nonbonded pdb=" N ASP B 145 " pdb=" OD1 ASP B 145 " model vdw 2.425 2.520 nonbonded pdb=" N THR B 52 " pdb=" N LEU B 53 " model vdw 2.439 2.560 ... (remaining 90657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 7.390 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.160 Find NCS groups from input model: 0.550 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 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 : 0.018 0.117 11116 Z= 1.226 Angle : 1.880 14.020 15082 Z= 1.274 Chirality : 0.101 0.484 1768 Planarity : 0.009 0.031 1964 Dihedral : 10.723 87.702 4170 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1434 helix: -1.40 (0.20), residues: 468 sheet: 0.55 (0.44), residues: 148 loop : -1.03 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.006 TRP A 180 HIS 0.007 0.002 HIS B 679 PHE 0.015 0.006 PHE A 153 TYR 0.055 0.010 TYR A 196 ARG 0.011 0.001 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8612 (mt) cc_final: 0.7663 (mt) REVERT: A 219 LYS cc_start: 0.5665 (pttm) cc_final: 0.5447 (pttt) REVERT: A 220 ASN cc_start: 0.8048 (m-40) cc_final: 0.7675 (m-40) REVERT: A 303 ASP cc_start: 0.8251 (m-30) cc_final: 0.7828 (t0) REVERT: A 336 ILE cc_start: 0.7906 (mm) cc_final: 0.7660 (mm) REVERT: A 386 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7364 (mmm-85) REVERT: A 448 ASN cc_start: 0.5545 (t0) cc_final: 0.4762 (t0) REVERT: A 508 MET cc_start: 0.6755 (mmp) cc_final: 0.6046 (mtp) REVERT: A 521 VAL cc_start: 0.9024 (t) cc_final: 0.8817 (m) REVERT: A 645 HIS cc_start: 0.7096 (t70) cc_final: 0.6788 (t70) REVERT: A 697 MET cc_start: 0.5428 (mtp) cc_final: 0.5200 (mtp) REVERT: B 21 ILE cc_start: 0.8600 (mt) cc_final: 0.7604 (mt) REVERT: B 220 ASN cc_start: 0.8142 (m-40) cc_final: 0.7686 (m-40) REVERT: B 303 ASP cc_start: 0.8182 (m-30) cc_final: 0.7754 (t0) REVERT: B 336 ILE cc_start: 0.7699 (mm) cc_final: 0.7329 (mm) REVERT: B 386 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7501 (mmm-85) REVERT: B 421 LEU cc_start: 0.8834 (mt) cc_final: 0.8589 (mt) REVERT: B 476 PHE cc_start: 0.8317 (m-80) cc_final: 0.8076 (m-80) REVERT: B 508 MET cc_start: 0.6708 (mmp) cc_final: 0.6387 (mtp) REVERT: B 521 VAL cc_start: 0.8982 (t) cc_final: 0.8615 (m) REVERT: B 645 HIS cc_start: 0.7025 (t70) cc_final: 0.6692 (t70) REVERT: B 695 ASN cc_start: 0.8509 (m-40) cc_final: 0.8307 (m110) REVERT: B 697 MET cc_start: 0.5703 (mtp) cc_final: 0.5261 (mtp) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2853 time to fit residues: 160.7847 Evaluate side-chains 245 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 86 HIS ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 481 GLN A 679 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 86 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 679 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11116 Z= 0.252 Angle : 0.767 9.960 15082 Z= 0.408 Chirality : 0.048 0.220 1768 Planarity : 0.005 0.071 1964 Dihedral : 7.179 58.843 1620 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.74 % Favored : 92.12 % Rotamer: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1434 helix: -0.29 (0.23), residues: 472 sheet: -0.18 (0.48), residues: 116 loop : -1.35 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 677 HIS 0.007 0.001 HIS B 456 PHE 0.016 0.003 PHE B 153 TYR 0.012 0.002 TYR B 617 ARG 0.007 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8512 (t) cc_final: 0.8090 (p) REVERT: A 409 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6525 (mtpt) REVERT: A 508 MET cc_start: 0.6588 (mmp) cc_final: 0.6276 (mtp) REVERT: A 521 VAL cc_start: 0.8964 (t) cc_final: 0.8757 (m) REVERT: A 577 ASN cc_start: 0.6982 (t0) cc_final: 0.6636 (p0) REVERT: A 645 HIS cc_start: 0.7559 (t70) cc_final: 0.7175 (t70) REVERT: A 695 ASN cc_start: 0.8372 (m-40) cc_final: 0.7996 (m110) REVERT: B 170 VAL cc_start: 0.8505 (t) cc_final: 0.8168 (p) REVERT: B 386 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.6497 (mtt180) REVERT: B 409 LYS cc_start: 0.7079 (mtmt) cc_final: 0.6811 (mtpt) REVERT: B 428 PHE cc_start: 0.7480 (t80) cc_final: 0.6965 (t80) REVERT: B 498 CYS cc_start: 0.8376 (t) cc_final: 0.8124 (t) REVERT: B 508 MET cc_start: 0.6644 (mmp) cc_final: 0.6394 (mtp) REVERT: B 577 ASN cc_start: 0.6946 (t0) cc_final: 0.6668 (p0) REVERT: B 692 ASN cc_start: 0.5947 (m-40) cc_final: 0.5609 (t0) REVERT: B 695 ASN cc_start: 0.8252 (m-40) cc_final: 0.7976 (m110) outliers start: 2 outliers final: 2 residues processed: 305 average time/residue: 0.2668 time to fit residues: 112.5626 Evaluate side-chains 214 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 HIS ** B 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11116 Z= 0.443 Angle : 0.993 10.164 15082 Z= 0.530 Chirality : 0.055 0.228 1768 Planarity : 0.007 0.083 1964 Dihedral : 8.888 60.920 1620 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.58 % Favored : 88.21 % Rotamer: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1434 helix: -0.94 (0.22), residues: 480 sheet: -1.30 (0.39), residues: 168 loop : -1.91 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 180 HIS 0.013 0.003 HIS B 504 PHE 0.032 0.005 PHE A 698 TYR 0.024 0.003 TYR A 617 ARG 0.010 0.001 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7417 (mtm180) REVERT: A 220 ASN cc_start: 0.8485 (m-40) cc_final: 0.7947 (m-40) REVERT: A 352 MET cc_start: 0.5884 (ptp) cc_final: 0.5660 (ptt) REVERT: A 421 LEU cc_start: 0.9142 (mt) cc_final: 0.8872 (mp) REVERT: A 521 VAL cc_start: 0.9308 (t) cc_final: 0.9058 (m) REVERT: A 694 GLU cc_start: 0.8797 (pm20) cc_final: 0.8174 (pm20) REVERT: B 89 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7339 (mtm180) REVERT: B 200 ILE cc_start: 0.8783 (mt) cc_final: 0.8541 (mm) REVERT: B 220 ASN cc_start: 0.8723 (m-40) cc_final: 0.8258 (m-40) REVERT: B 386 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.7041 (mtt90) REVERT: B 402 ASP cc_start: 0.8367 (p0) cc_final: 0.8074 (p0) REVERT: B 421 LEU cc_start: 0.9086 (mt) cc_final: 0.8808 (mp) REVERT: B 446 GLU cc_start: 0.8813 (tt0) cc_final: 0.8520 (tt0) REVERT: B 461 GLU cc_start: 0.8804 (tp30) cc_final: 0.8539 (tm-30) REVERT: B 521 VAL cc_start: 0.9241 (t) cc_final: 0.8889 (m) REVERT: B 692 ASN cc_start: 0.6613 (m-40) cc_final: 0.6210 (t0) REVERT: B 695 ASN cc_start: 0.8512 (m-40) cc_final: 0.7982 (m110) outliers start: 3 outliers final: 0 residues processed: 245 average time/residue: 0.2707 time to fit residues: 89.5703 Evaluate side-chains 182 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 645 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11116 Z= 0.229 Angle : 0.725 7.883 15082 Z= 0.383 Chirality : 0.047 0.179 1768 Planarity : 0.005 0.077 1964 Dihedral : 7.880 57.510 1620 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1434 helix: -0.12 (0.24), residues: 474 sheet: -0.94 (0.41), residues: 154 loop : -1.95 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 677 HIS 0.006 0.001 HIS B 504 PHE 0.017 0.002 PHE A 153 TYR 0.018 0.001 TYR A 617 ARG 0.011 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8613 (t) cc_final: 0.8245 (p) REVERT: A 220 ASN cc_start: 0.8561 (m-40) cc_final: 0.8070 (m-40) REVERT: A 421 LEU cc_start: 0.9073 (mt) cc_final: 0.8795 (mp) REVERT: A 446 GLU cc_start: 0.8897 (tt0) cc_final: 0.8649 (pt0) REVERT: A 527 VAL cc_start: 0.8221 (p) cc_final: 0.7981 (m) REVERT: A 694 GLU cc_start: 0.8228 (pm20) cc_final: 0.7726 (pm20) REVERT: B 89 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7229 (mtt180) REVERT: B 156 TYR cc_start: 0.7735 (m-80) cc_final: 0.7331 (m-80) REVERT: B 170 VAL cc_start: 0.8622 (t) cc_final: 0.8230 (p) REVERT: B 220 ASN cc_start: 0.8496 (m-40) cc_final: 0.8189 (m-40) REVERT: B 694 GLU cc_start: 0.8694 (pm20) cc_final: 0.8101 (pm20) REVERT: B 697 MET cc_start: 0.6761 (mmm) cc_final: 0.6216 (mmm) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.2447 time to fit residues: 79.3550 Evaluate side-chains 189 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0060 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS B 645 HIS B 679 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11116 Z= 0.168 Angle : 0.668 8.079 15082 Z= 0.350 Chirality : 0.046 0.176 1768 Planarity : 0.004 0.073 1964 Dihedral : 7.263 55.268 1620 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1434 helix: 0.06 (0.24), residues: 474 sheet: -0.69 (0.42), residues: 142 loop : -1.94 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 677 HIS 0.011 0.001 HIS B 629 PHE 0.018 0.002 PHE A 698 TYR 0.014 0.001 TYR A 617 ARG 0.003 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8542 (t) cc_final: 0.8089 (p) REVERT: A 220 ASN cc_start: 0.8479 (m-40) cc_final: 0.8092 (m-40) REVERT: A 409 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7194 (ptmt) REVERT: A 446 GLU cc_start: 0.8903 (tt0) cc_final: 0.8687 (pt0) REVERT: A 541 MET cc_start: 0.5070 (mmp) cc_final: 0.4039 (mmt) REVERT: A 608 THR cc_start: 0.6985 (m) cc_final: 0.6538 (m) REVERT: B 130 MET cc_start: 0.3723 (mmt) cc_final: 0.3503 (mmt) REVERT: B 156 TYR cc_start: 0.7710 (m-80) cc_final: 0.7482 (m-80) REVERT: B 170 VAL cc_start: 0.8541 (t) cc_final: 0.8130 (p) REVERT: B 220 ASN cc_start: 0.8494 (m-40) cc_final: 0.8093 (m-40) REVERT: B 409 LYS cc_start: 0.7601 (mtmt) cc_final: 0.6984 (ptmt) REVERT: B 694 GLU cc_start: 0.8662 (pm20) cc_final: 0.8152 (pm20) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2279 time to fit residues: 77.6638 Evaluate side-chains 185 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.9504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11116 Z= 0.360 Angle : 0.845 9.334 15082 Z= 0.446 Chirality : 0.051 0.246 1768 Planarity : 0.005 0.075 1964 Dihedral : 8.405 61.325 1620 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.55 % Favored : 87.31 % Rotamer: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1434 helix: -0.54 (0.23), residues: 480 sheet: -0.66 (0.43), residues: 142 loop : -2.13 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.014 0.002 HIS A 30 PHE 0.034 0.004 PHE A 698 TYR 0.022 0.002 TYR A 617 ARG 0.008 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.2961 (OUTLIER) cc_final: 0.1518 (mt0) REVERT: A 118 GLU cc_start: 0.5371 (pm20) cc_final: 0.4426 (pt0) REVERT: A 160 PHE cc_start: 0.7701 (m-10) cc_final: 0.6905 (m-10) REVERT: A 220 ASN cc_start: 0.8751 (m-40) cc_final: 0.8463 (m-40) REVERT: B 118 GLU cc_start: 0.4040 (pm20) cc_final: 0.3796 (pm20) REVERT: B 156 TYR cc_start: 0.7835 (m-10) cc_final: 0.7387 (m-80) REVERT: B 220 ASN cc_start: 0.8612 (m-40) cc_final: 0.8296 (m-40) REVERT: B 476 PHE cc_start: 0.8981 (m-80) cc_final: 0.8742 (m-80) REVERT: B 505 ILE cc_start: 0.9001 (mt) cc_final: 0.8783 (tt) REVERT: B 694 GLU cc_start: 0.8707 (pm20) cc_final: 0.8286 (pm20) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2260 time to fit residues: 66.4687 Evaluate side-chains 162 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.9822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11116 Z= 0.243 Angle : 0.726 8.206 15082 Z= 0.380 Chirality : 0.048 0.232 1768 Planarity : 0.005 0.074 1964 Dihedral : 7.877 55.759 1620 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.41 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1434 helix: -0.22 (0.24), residues: 466 sheet: -0.53 (0.41), residues: 164 loop : -2.15 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 180 HIS 0.007 0.001 HIS A 30 PHE 0.027 0.002 PHE A 698 TYR 0.018 0.002 TYR A 617 ARG 0.005 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8677 (t) cc_final: 0.8382 (p) REVERT: A 220 ASN cc_start: 0.8676 (m-40) cc_final: 0.8344 (m-40) REVERT: A 342 ASP cc_start: 0.6516 (t70) cc_final: 0.5983 (t70) REVERT: A 366 LEU cc_start: 0.7982 (pp) cc_final: 0.7476 (tt) REVERT: A 409 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7706 (ptmt) REVERT: B 52 THR cc_start: 0.4296 (p) cc_final: 0.3843 (m) REVERT: B 170 VAL cc_start: 0.8723 (t) cc_final: 0.8423 (p) REVERT: B 220 ASN cc_start: 0.8602 (m-40) cc_final: 0.8213 (m-40) REVERT: B 541 MET cc_start: 0.5745 (mmp) cc_final: 0.5173 (mmm) REVERT: B 694 GLU cc_start: 0.8716 (pm20) cc_final: 0.8339 (pm20) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2342 time to fit residues: 72.2514 Evaluate side-chains 172 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 629 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 1.0092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11116 Z= 0.216 Angle : 0.726 20.373 15082 Z= 0.373 Chirality : 0.048 0.185 1768 Planarity : 0.005 0.071 1964 Dihedral : 7.676 56.536 1620 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.13 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.97 (0.22), residues: 1434 helix: -0.14 (0.24), residues: 458 sheet: -1.00 (0.40), residues: 172 loop : -2.16 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 180 HIS 0.007 0.001 HIS A 504 PHE 0.024 0.003 PHE A 698 TYR 0.014 0.001 TYR B 617 ARG 0.006 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8674 (t) cc_final: 0.8340 (p) REVERT: A 220 ASN cc_start: 0.8752 (m-40) cc_final: 0.8261 (t0) REVERT: A 330 HIS cc_start: 0.5912 (m90) cc_final: 0.5622 (m170) REVERT: A 409 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7647 (ptmt) REVERT: A 541 MET cc_start: 0.5314 (mmp) cc_final: 0.4313 (mmt) REVERT: A 562 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8213 (tmm-80) REVERT: B 156 TYR cc_start: 0.7793 (m-10) cc_final: 0.7435 (m-80) REVERT: B 170 VAL cc_start: 0.8696 (t) cc_final: 0.8417 (p) REVERT: B 220 ASN cc_start: 0.8458 (m-40) cc_final: 0.8199 (m-40) REVERT: B 541 MET cc_start: 0.5676 (mmp) cc_final: 0.5391 (mmp) REVERT: B 677 TRP cc_start: 0.4807 (m-10) cc_final: 0.4454 (m-10) REVERT: B 694 GLU cc_start: 0.8710 (pm20) cc_final: 0.8315 (pm20) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2000 time to fit residues: 64.4754 Evaluate side-chains 161 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 1.0311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11116 Z= 0.203 Angle : 0.691 10.130 15082 Z= 0.359 Chirality : 0.047 0.189 1768 Planarity : 0.005 0.070 1964 Dihedral : 7.522 56.122 1620 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.72 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.22), residues: 1434 helix: -0.20 (0.24), residues: 462 sheet: -0.99 (0.39), residues: 172 loop : -2.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 180 HIS 0.006 0.001 HIS A 504 PHE 0.044 0.003 PHE A 720 TYR 0.015 0.001 TYR B 617 ARG 0.006 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6020 (mmt180) cc_final: 0.5773 (mmt180) REVERT: A 170 VAL cc_start: 0.8575 (t) cc_final: 0.8274 (p) REVERT: A 220 ASN cc_start: 0.8676 (m-40) cc_final: 0.8405 (m-40) REVERT: A 409 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7937 (mtmt) REVERT: A 541 MET cc_start: 0.5447 (mmp) cc_final: 0.4353 (mmt) REVERT: B 156 TYR cc_start: 0.7714 (m-10) cc_final: 0.7463 (m-80) REVERT: B 170 VAL cc_start: 0.8674 (t) cc_final: 0.8367 (p) REVERT: B 541 MET cc_start: 0.5699 (mmp) cc_final: 0.5451 (mmp) REVERT: B 677 TRP cc_start: 0.4677 (m-10) cc_final: 0.4352 (m-10) REVERT: B 694 GLU cc_start: 0.8578 (pm20) cc_final: 0.8367 (pm20) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2096 time to fit residues: 66.4148 Evaluate side-chains 163 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.0010 chunk 120 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 1.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11116 Z= 0.193 Angle : 0.681 7.245 15082 Z= 0.354 Chirality : 0.047 0.191 1768 Planarity : 0.004 0.070 1964 Dihedral : 7.079 52.893 1620 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1434 helix: -0.17 (0.24), residues: 460 sheet: -0.94 (0.39), residues: 172 loop : -2.20 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 677 HIS 0.004 0.001 HIS A 86 PHE 0.044 0.003 PHE B 283 TYR 0.014 0.001 TYR B 617 ARG 0.006 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6189 (mmt) cc_final: 0.5912 (mmm) REVERT: A 170 VAL cc_start: 0.8557 (t) cc_final: 0.8264 (p) REVERT: A 220 ASN cc_start: 0.8620 (m-40) cc_final: 0.8278 (m-40) REVERT: A 226 LEU cc_start: 0.8225 (mt) cc_final: 0.7987 (mt) REVERT: A 330 HIS cc_start: 0.5910 (m90) cc_final: 0.5601 (m170) REVERT: A 541 MET cc_start: 0.5449 (mmp) cc_final: 0.4379 (mmt) REVERT: B 156 TYR cc_start: 0.7726 (m-10) cc_final: 0.7453 (m-80) REVERT: B 170 VAL cc_start: 0.8646 (t) cc_final: 0.8346 (p) REVERT: B 220 ASN cc_start: 0.8495 (m-40) cc_final: 0.8201 (t0) REVERT: B 330 HIS cc_start: 0.6273 (m90) cc_final: 0.5925 (m90) REVERT: B 541 MET cc_start: 0.5898 (mmp) cc_final: 0.5430 (mmp) REVERT: B 600 VAL cc_start: 0.8720 (t) cc_final: 0.8498 (p) REVERT: B 694 GLU cc_start: 0.8630 (pm20) cc_final: 0.8390 (pm20) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1933 time to fit residues: 61.3633 Evaluate side-chains 163 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.165517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135479 restraints weight = 26749.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138377 restraints weight = 18592.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140388 restraints weight = 14237.593| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 1.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11116 Z= 0.185 Angle : 0.667 8.903 15082 Z= 0.348 Chirality : 0.047 0.191 1768 Planarity : 0.004 0.068 1964 Dihedral : 6.879 53.239 1620 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.44 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1434 helix: -0.18 (0.24), residues: 460 sheet: -0.99 (0.39), residues: 174 loop : -2.25 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 180 HIS 0.003 0.001 HIS A 504 PHE 0.036 0.003 PHE B 283 TYR 0.014 0.001 TYR B 617 ARG 0.006 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.57 seconds wall clock time: 46 minutes 31.84 seconds (2791.84 seconds total)