Starting phenix.real_space_refine (version: dev) on Mon Dec 12 15:42:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/12_2022/7lgm_23327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/12_2022/7lgm_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_23327/12_2022/7lgm_23327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/12_2022/7lgm_23327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/12_2022/7lgm_23327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgm_23327/12_2022/7lgm_23327_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 6.68, per 1000 atoms: 0.61 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: 4.60 Conformation dependent library (CDL) restraints added in 1.7 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: 1.54 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: 3.40 Time building geometry restraints manager: 4.95 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: 6457 17.54 - 35.08: 202 35.08 - 52.62: 39 52.62 - 70.16: 14 70.16 - 87.70: 4 Dihedral angle restraints: 6716 sinusoidal: 2632 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 6713 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 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. 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.560 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 31.980 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 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 : 9.930 87.702 4108 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.213 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 outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2500 time to fit residues: 140.8446 Evaluate side-chains 237 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7801 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 HIS A 220 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 448 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 679 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11116 Z= 0.243 Angle : 0.759 9.692 15082 Z= 0.404 Chirality : 0.047 0.221 1768 Planarity : 0.005 0.072 1964 Dihedral : 5.984 32.729 1558 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.74 % Favored : 92.12 % Rotamer Outliers : 0.34 % 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: -1.26 (0.21), residues: 1434 helix: -0.31 (0.23), residues: 472 sheet: -0.00 (0.48), residues: 116 loop : -1.28 (0.21), residues: 846 *********************** 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: 4 poor density : 301 time to evaluate : 1.630 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 outliers start: 4 outliers final: 2 residues processed: 304 average time/residue: 0.2374 time to fit residues: 100.7688 Evaluate side-chains 202 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1028 time to fit residues: 2.2044 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 139 optimal weight: 0.0970 chunk 115 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** 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 220 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 11116 Z= 0.438 Angle : 0.987 10.250 15082 Z= 0.530 Chirality : 0.055 0.273 1768 Planarity : 0.007 0.085 1964 Dihedral : 7.297 40.625 1558 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.81 % Favored : 88.91 % Rotamer Outliers : 0.43 % 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: -2.28 (0.20), residues: 1434 helix: -1.00 (0.22), residues: 480 sheet: -1.09 (0.41), residues: 164 loop : -1.96 (0.20), residues: 790 *********************** 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 248 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 247 average time/residue: 0.2736 time to fit residues: 91.1961 Evaluate side-chains 174 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6501 ------------------------------------------------------------------------------- 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: 0.7980 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.0030 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 679 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 695 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.8093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11116 Z= 0.262 Angle : 0.748 7.966 15082 Z= 0.397 Chirality : 0.049 0.174 1768 Planarity : 0.005 0.077 1964 Dihedral : 6.441 46.760 1558 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer Outliers : 0.00 % 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: -1.93 (0.21), residues: 1434 helix: -0.60 (0.23), residues: 486 sheet: -0.72 (0.42), residues: 154 loop : -1.88 (0.21), residues: 794 *********************** 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 220 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2323 time to fit residues: 71.8888 Evaluate side-chains 165 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7705 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 0 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.8446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11116 Z= 0.184 Angle : 0.673 7.148 15082 Z= 0.352 Chirality : 0.047 0.206 1768 Planarity : 0.005 0.074 1964 Dihedral : 5.786 48.302 1558 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer Outliers : 0.00 % 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: -1.67 (0.21), residues: 1434 helix: -0.16 (0.24), residues: 486 sheet: -0.62 (0.41), residues: 150 loop : -1.87 (0.21), residues: 798 *********************** 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 230 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2249 time to fit residues: 73.4832 Evaluate side-chains 169 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7562 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 629 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 HIS ** 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: 0.6379 moved from start: 0.8917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11116 Z= 0.233 Angle : 0.710 9.733 15082 Z= 0.370 Chirality : 0.050 0.688 1768 Planarity : 0.005 0.070 1964 Dihedral : 5.902 50.176 1558 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer Outliers : 0.00 % 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: -1.71 (0.22), residues: 1434 helix: -0.33 (0.24), residues: 486 sheet: -0.62 (0.38), residues: 172 loop : -1.83 (0.22), residues: 776 *********************** 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 210 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2071 time to fit residues: 62.7839 Evaluate side-chains 165 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6305 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.0270 chunk 136 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 84 optimal weight: 7.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** 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: 0.6336 moved from start: 0.9274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11116 Z= 0.189 Angle : 0.673 9.605 15082 Z= 0.351 Chirality : 0.047 0.183 1768 Planarity : 0.005 0.070 1964 Dihedral : 5.665 49.162 1558 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.02 % Favored : 88.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1434 helix: -0.37 (0.24), residues: 498 sheet: -0.49 (0.39), residues: 172 loop : -1.97 (0.21), residues: 764 *********************** 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 221 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.291 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 outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2294 time to fit residues: 72.8783 Evaluate side-chains 168 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8227 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 224 GLN ** 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: 0.6536 moved from start: 1.0095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 11116 Z= 0.306 Angle : 0.791 9.852 15082 Z= 0.418 Chirality : 0.051 0.242 1768 Planarity : 0.005 0.072 1964 Dihedral : 6.457 56.013 1558 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.76 % Favored : 87.10 % Rotamer Outliers : 0.00 % 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: -2.16 (0.21), residues: 1434 helix: -0.71 (0.23), residues: 500 sheet: -0.23 (0.42), residues: 154 loop : -2.24 (0.21), residues: 780 *********************** 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 209 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2254 time to fit residues: 67.8268 Evaluate side-chains 166 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6743 ------------------------------------------------------------------------------- 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: 0.8980 chunk 127 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN ** 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: 0.6428 moved from start: 1.0295 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= 0.207 Angle : 0.690 8.123 15082 Z= 0.361 Chirality : 0.048 0.204 1768 Planarity : 0.005 0.072 1964 Dihedral : 5.932 52.431 1558 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer Outliers : 0.00 % 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: -0.37 (0.24), residues: 496 sheet: -0.35 (0.42), residues: 160 loop : -2.23 (0.21), residues: 778 *********************** 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 211 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2120 time to fit residues: 64.3680 Evaluate side-chains 159 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6284 ------------------------------------------------------------------------------- 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: 0.4980 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 1.0532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11116 Z= 0.207 Angle : 0.706 7.944 15082 Z= 0.369 Chirality : 0.049 0.214 1768 Planarity : 0.005 0.071 1964 Dihedral : 5.798 51.454 1558 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.27 % Favored : 87.59 % Rotamer Outliers : 0.00 % 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: -2.09 (0.21), residues: 1434 helix: -0.53 (0.23), residues: 496 sheet: -0.83 (0.39), residues: 180 loop : -2.17 (0.21), residues: 758 ********************** 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 209 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2284 time to fit residues: 68.3704 Evaluate side-chains 158 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7661 ------------------------------------------------------------------------------- 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: 0.0370 chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 390 ASN ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.168483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138905 restraints weight = 26628.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.141754 restraints weight = 18566.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.143763 restraints weight = 14275.739| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 1.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11116 Z= 0.175 Angle : 0.670 9.487 15082 Z= 0.346 Chirality : 0.048 0.216 1768 Planarity : 0.005 0.070 1964 Dihedral : 5.420 47.956 1558 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.02 % Favored : 88.84 % Rotamer Outliers : 0.00 % 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: -2.19 (0.21), residues: 1434 helix: -0.52 (0.23), residues: 504 sheet: -0.91 (0.36), residues: 216 loop : -2.36 (0.22), residues: 714 =============================================================================== Job complete usr+sys time: 2371.74 seconds wall clock time: 43 minutes 44.59 seconds (2624.59 seconds total)