Starting phenix.real_space_refine on Mon Nov 13 23:44:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxf_12638/11_2023/7nxf_12638_updated.pdb" } resolution = 3.1 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= 0.001 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 2 5.49 5 Mg 1 5.21 5 S 23 5.16 5 C 4130 2.51 5 N 1060 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A GLU 903": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6405 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6405 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'peptide': 829, 'undetermined': 3} Link IDs: {'PTRANS': 31, 'TRANS': 797, None: 3} Not linked: pdbres="GLN A 920 " pdbres="ADP A1001 " Not linked: pdbres="ADP A1001 " pdbres=" MG A1002 " Not linked: pdbres=" MG A1002 " pdbres=" K A1003 " Chain breaks: 2 Time building chain proxies: 4.29, per 1000 atoms: 0.67 Number of scatterers: 6405 At special positions: 0 Unit cell: (92.07, 72.819, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 23 16.00 P 2 15.00 Mg 1 11.99 O 1188 8.00 N 1060 7.00 C 4130 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 6 sheets defined 48.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.732A pdb=" N PHE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 143 through 176 removed outlier: 3.857A pdb=" N ASP A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 314 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.571A pdb=" N ILE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.572A pdb=" N ALA A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.929A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.635A pdb=" N LEU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.518A pdb=" N GLN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.850A pdb=" N THR A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 Processing helix chain 'A' and resid 581 through 584 No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 594 through 602 removed outlier: 3.822A pdb=" N ASP A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.746A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 671 through 713 removed outlier: 3.993A pdb=" N LEU A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 752 through 780 removed outlier: 3.686A pdb=" N MET A 777 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 812 removed outlier: 3.686A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 811 " --> pdb=" O TRP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 844 Processing helix chain 'A' and resid 854 through 879 removed outlier: 3.661A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 918 Processing sheet with id= A, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL A 204 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 256 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 214 through 216 Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 Processing sheet with id= D, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.667A pdb=" N ILE A 374 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 632 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 376 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 553 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER A 377 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS A 555 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 579 " --> pdb=" O GLY A 606 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 525 through 532 removed outlier: 3.937A pdb=" N GLU A 525 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 517 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 515 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 529 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 513 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG A 511 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.566A pdb=" N ARG A 253 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 251 " --> pdb=" O ASP A 226 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 882 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: 1.95 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1504 1.33 - 1.45: 1404 1.45 - 1.58: 3585 1.58 - 1.70: 0 1.70 - 1.83: 40 Bond restraints: 6533 Sorted by residual: bond pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sigma weight residual 1.610 1.808 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.401 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C8 ADP A1001 " pdb=" N9 ADP A1001 " ideal model delta sigma weight residual 1.337 1.409 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 1.426 1.354 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 6528 not shown) Histogram of bond angle deviations from ideal: 88.40 - 97.52: 2 97.52 - 106.64: 178 106.64 - 115.76: 4130 115.76 - 124.88: 4458 124.88 - 134.00: 108 Bond angle restraints: 8876 Sorted by residual: angle pdb=" O1A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O2A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O3A ADP A1001 " ideal model delta sigma weight residual 108.20 123.77 -15.57 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 120.50 105.39 15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" PA ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sigma weight residual 120.50 106.19 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" O3B ADP A1001 " ideal model delta sigma weight residual 108.20 94.68 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 8871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 3744 30.30 - 60.60: 109 60.60 - 90.90: 4 90.90 - 121.20: 0 121.20 - 151.50: 2 Dihedral angle restraints: 3859 sinusoidal: 1498 harmonic: 2361 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 74.18 -134.18 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" CA VAL A 93 " pdb=" C VAL A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta harmonic sigma weight residual 180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 3856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 685 0.038 - 0.076: 264 0.076 - 0.114: 73 0.114 - 0.152: 13 0.152 - 0.190: 4 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C2' ADP A1001 " pdb=" C1' ADP A1001 " pdb=" C3' ADP A1001 " pdb=" O2' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CB THR A 267 " pdb=" CA THR A 267 " pdb=" OG1 THR A 267 " pdb=" CG2 THR A 267 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CG LEU A 702 " pdb=" CB LEU A 702 " pdb=" CD1 LEU A 702 " pdb=" CD2 LEU A 702 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 1036 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A 709 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 592 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 593 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 846 " -0.023 2.00e-02 2.50e+03 1.89e-02 8.94e+00 pdb=" CG TRP A 846 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 846 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 846 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 846 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 846 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 846 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 846 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 846 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 846 " -0.003 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 2215 2.85 - 3.42: 7273 3.42 - 4.00: 11445 4.00 - 4.57: 16585 4.57 - 5.14: 23454 Nonbonded interactions: 60972 Sorted by model distance: nonbonded pdb=" O PHE A 246 " pdb=" OG SER A 249 " model vdw 2.281 2.440 nonbonded pdb=" O THR A 773 " pdb=" OG1 THR A 776 " model vdw 2.343 2.440 nonbonded pdb=" OE2 GLU A 602 " pdb=" OH TYR A 627 " model vdw 2.388 2.440 nonbonded pdb=" O4' ADP A1001 " pdb=" O5' ADP A1001 " model vdw 2.391 2.432 nonbonded pdb=" OD2 ASP A 403 " pdb=" OG1 THR A 407 " model vdw 2.394 2.440 ... (remaining 60967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 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: 11.140 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.006 0.216 6533 Z= 0.391 Angle : 0.816 19.804 8876 Z= 0.391 Chirality : 0.044 0.190 1039 Planarity : 0.005 0.082 1118 Dihedral : 14.198 151.503 2345 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.29), residues: 823 helix: 0.88 (0.25), residues: 424 sheet: -1.48 (0.68), residues: 53 loop : -2.07 (0.32), residues: 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2729 time to fit residues: 26.5237 Evaluate side-chains 44 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6533 Z= 0.282 Angle : 0.653 7.089 8876 Z= 0.324 Chirality : 0.042 0.147 1039 Planarity : 0.004 0.060 1118 Dihedral : 8.285 135.502 888 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.46 % Allowed : 8.33 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 823 helix: 1.35 (0.26), residues: 425 sheet: -1.47 (0.68), residues: 52 loop : -2.28 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.2177 time to fit residues: 16.0722 Evaluate side-chains 52 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0752 time to fit residues: 1.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 244 GLN A 683 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6533 Z= 0.211 Angle : 0.599 6.439 8876 Z= 0.297 Chirality : 0.041 0.150 1039 Planarity : 0.004 0.053 1118 Dihedral : 7.883 131.319 888 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.02 % Allowed : 12.13 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 823 helix: 1.67 (0.26), residues: 431 sheet: -1.52 (0.68), residues: 49 loop : -2.22 (0.31), residues: 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.2148 time to fit residues: 15.2595 Evaluate side-chains 52 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0721 time to fit residues: 1.5749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 806 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6533 Z= 0.337 Angle : 0.634 6.259 8876 Z= 0.314 Chirality : 0.042 0.142 1039 Planarity : 0.004 0.047 1118 Dihedral : 7.684 126.692 888 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.90 % Allowed : 13.01 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.30), residues: 823 helix: 1.72 (0.26), residues: 435 sheet: -1.74 (0.63), residues: 52 loop : -2.14 (0.31), residues: 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 53 average time/residue: 0.2015 time to fit residues: 14.8155 Evaluate side-chains 49 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0707 time to fit residues: 1.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 0.5246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6533 Z= 0.144 Angle : 0.571 6.597 8876 Z= 0.281 Chirality : 0.040 0.135 1039 Planarity : 0.004 0.049 1118 Dihedral : 7.333 124.295 888 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.02 % Allowed : 14.77 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 823 helix: 1.98 (0.26), residues: 433 sheet: -1.56 (0.65), residues: 52 loop : -2.13 (0.31), residues: 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.745 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 56 average time/residue: 0.1828 time to fit residues: 14.4382 Evaluate side-chains 48 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0672 time to fit residues: 1.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 6533 Z= 0.500 Angle : 0.704 6.810 8876 Z= 0.350 Chirality : 0.044 0.128 1039 Planarity : 0.004 0.048 1118 Dihedral : 7.461 120.961 888 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.90 % Allowed : 15.06 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.30), residues: 823 helix: 1.79 (0.26), residues: 437 sheet: -1.47 (0.64), residues: 51 loop : -2.15 (0.32), residues: 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.2267 time to fit residues: 16.0432 Evaluate side-chains 51 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1320 time to fit residues: 2.8011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6533 Z= 0.170 Angle : 0.592 9.088 8876 Z= 0.288 Chirality : 0.040 0.132 1039 Planarity : 0.004 0.058 1118 Dihedral : 7.157 119.379 888 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.88 % Allowed : 16.08 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.31), residues: 823 helix: 1.92 (0.26), residues: 434 sheet: -1.66 (0.64), residues: 54 loop : -2.10 (0.32), residues: 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.2150 time to fit residues: 14.0401 Evaluate side-chains 44 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0743 time to fit residues: 1.4499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6533 Z= 0.173 Angle : 0.579 8.321 8876 Z= 0.281 Chirality : 0.040 0.131 1039 Planarity : 0.004 0.060 1118 Dihedral : 6.792 117.130 888 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.44 % Allowed : 17.25 % Favored : 82.31 % 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: 0.29 (0.31), residues: 823 helix: 2.06 (0.26), residues: 428 sheet: -1.51 (0.66), residues: 56 loop : -2.08 (0.31), residues: 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.726 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1826 time to fit residues: 12.1787 Evaluate side-chains 43 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0638 time to fit residues: 1.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 0.0040 chunk 48 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6533 Z= 0.201 Angle : 0.576 7.707 8876 Z= 0.279 Chirality : 0.040 0.150 1039 Planarity : 0.004 0.052 1118 Dihedral : 6.574 117.694 888 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.29 % Allowed : 17.11 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 823 helix: 2.11 (0.26), residues: 428 sheet: -1.38 (0.67), residues: 55 loop : -2.04 (0.31), residues: 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.2053 time to fit residues: 12.6339 Evaluate side-chains 44 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0646 time to fit residues: 1.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6533 Z= 0.181 Angle : 0.581 9.681 8876 Z= 0.278 Chirality : 0.041 0.162 1039 Planarity : 0.003 0.043 1118 Dihedral : 6.451 122.033 888 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.15 % Allowed : 17.54 % Favored : 82.31 % 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: 0.45 (0.31), residues: 823 helix: 2.16 (0.26), residues: 428 sheet: -1.31 (0.68), residues: 55 loop : -1.99 (0.31), residues: 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1854 time to fit residues: 12.1087 Evaluate side-chains 43 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 1.1529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.089751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060160 restraints weight = 18814.733| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.29 r_work: 0.2990 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6533 Z= 0.316 Angle : 0.627 8.600 8876 Z= 0.304 Chirality : 0.042 0.143 1039 Planarity : 0.004 0.043 1118 Dihedral : 6.565 129.505 888 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.29 % Allowed : 16.96 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 823 helix: 2.11 (0.26), residues: 434 sheet: -1.33 (0.68), residues: 55 loop : -2.01 (0.32), residues: 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.97 seconds wall clock time: 30 minutes 12.80 seconds (1812.80 seconds total)