Starting phenix.real_space_refine on Fri Jan 19 10:49:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl1_22369/01_2024/7jl1_22369_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4056 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 1 5.89 5 P 30 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4451 2.51 5 N 1220 2.21 5 O 1383 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7132 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5184 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 25, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "X" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Y" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1319 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4362 SG CYS A 810 69.713 98.163 31.557 1.00 61.48 S ATOM 4388 SG CYS A 813 72.965 99.873 31.865 1.00 62.37 S ATOM 4728 SG CYS A 864 71.899 99.040 28.358 1.00 71.24 S ATOM 4767 SG CYS A 869 72.980 96.306 30.728 1.00 76.60 S Time building chain proxies: 4.72, per 1000 atoms: 0.66 Number of scatterers: 7132 At special positions: 0 Unit cell: (96.9088, 121.918, 67.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 41 16.00 P 30 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1383 8.00 N 1220 7.00 C 4451 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: 2.93 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 813 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 869 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 864 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 810 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 36.6% alpha, 14.4% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.719A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.616A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.763A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.377A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 removed outlier: 3.902A pdb=" N ILE A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 594 through 602 removed outlier: 3.618A pdb=" N ARG A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 removed outlier: 3.577A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.838A pdb=" N ARG A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 removed outlier: 3.544A pdb=" N GLN A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 769 " --> pdb=" O ILE A 765 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 793 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 438 through 441 removed outlier: 6.347A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.727A pdb=" N VAL A 712 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 741 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 714 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 892 through 895 removed outlier: 6.973A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 874 through 879 Processing sheet with id= F, first strand: chain 'B' and resid 272 through 274 removed outlier: 3.990A pdb=" N ILE B 426 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 316 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 390 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 301 through 303 removed outlier: 4.273A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 357 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 361 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 390 through 392 266 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1329 1.32 - 1.45: 1908 1.45 - 1.57: 3981 1.57 - 1.69: 57 1.69 - 1.81: 60 Bond restraints: 7335 Sorted by residual: bond pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" F4 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.684 1.768 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N CYS A 490 " pdb=" CA CYS A 490 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.33e-02 5.65e+03 7.06e+00 ... (remaining 7330 not shown) Histogram of bond angle deviations from ideal: 88.94 - 106.77: 369 106.77 - 124.60: 9466 124.60 - 142.43: 221 142.43 - 160.26: 0 160.26 - 178.09: 2 Bond angle restraints: 10058 Sorted by residual: angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F2 ALF A2002 " ideal model delta sigma weight residual 108.68 178.09 -69.41 3.00e+00 1.11e-01 5.35e+02 angle pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.63 177.66 -68.03 3.00e+00 1.11e-01 5.14e+02 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F3 ALF A2002 " ideal model delta sigma weight residual 109.59 88.94 20.65 3.00e+00 1.11e-01 4.74e+01 angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.02 88.94 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 110.21 91.34 18.87 3.00e+00 1.11e-01 3.96e+01 ... (remaining 10053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 4274 35.43 - 70.85: 116 70.85 - 106.28: 11 106.28 - 141.70: 2 141.70 - 177.12: 3 Dihedral angle restraints: 4406 sinusoidal: 1987 harmonic: 2419 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 56.28 -116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA THR A 347 " pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 877 0.061 - 0.121: 251 0.121 - 0.182: 32 0.182 - 0.243: 2 0.243 - 0.303: 2 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C3' G Y 4 " pdb=" C4' G Y 4 " pdb=" O3' G Y 4 " pdb=" C2' G Y 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' A X 2 " pdb=" C4' A X 2 " pdb=" O3' A X 2 " pdb=" C2' A X 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU A 493 " pdb=" N LEU A 493 " pdb=" C LEU A 493 " pdb=" CB LEU A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 1161 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 2 " 0.042 2.00e-02 2.50e+03 1.85e-02 9.43e+00 pdb=" N9 A X 2 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A X 2 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A X 2 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A X 2 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A X 2 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A X 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 2 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A X 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 313 " 0.015 2.00e-02 2.50e+03 1.72e-02 4.46e+00 pdb=" CG HIS B 313 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 313 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 313 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 313 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 411 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO B 412 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.028 5.00e-02 4.00e+02 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 3995 3.00 - 3.63: 9965 3.63 - 4.27: 14973 4.27 - 4.90: 25085 Nonbonded interactions: 54032 Sorted by model distance: nonbonded pdb=" F1 ALF A2002 " pdb="MG MG A2003 " model vdw 1.727 2.120 nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2003 " model vdw 1.793 2.170 nonbonded pdb=" F4 ALF A2002 " pdb="MG MG A2003 " model vdw 1.813 2.120 nonbonded pdb=" O1B ADP A2001 " pdb=" F4 ALF A2002 " model vdw 2.014 2.390 nonbonded pdb=" O2B ADP A2001 " pdb=" F2 ALF A2002 " model vdw 2.064 2.390 ... (remaining 54027 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.170 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.940 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.011 0.114 7335 Z= 0.705 Angle : 1.382 69.407 10058 Z= 0.600 Chirality : 0.054 0.303 1164 Planarity : 0.005 0.050 1158 Dihedral : 16.789 177.125 2830 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % 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 (0.29), residues: 805 helix: 1.22 (0.30), residues: 302 sheet: 0.06 (0.45), residues: 144 loop : -0.35 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 315 HIS 0.020 0.002 HIS B 313 PHE 0.019 0.003 PHE A 295 TYR 0.031 0.003 TYR A 303 ARG 0.014 0.001 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8411 (tppt) cc_final: 0.8197 (ttpt) REVERT: A 387 MET cc_start: 0.8925 (mmp) cc_final: 0.8701 (mmt) REVERT: A 435 ASP cc_start: 0.8639 (t0) cc_final: 0.7757 (t0) REVERT: A 492 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (p0) REVERT: A 610 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7415 (mtpp) REVERT: A 690 ASP cc_start: 0.8452 (p0) cc_final: 0.8165 (p0) REVERT: A 692 ASN cc_start: 0.8152 (m-40) cc_final: 0.7544 (t0) REVERT: A 756 TYR cc_start: 0.7623 (t80) cc_final: 0.7403 (t80) REVERT: A 761 MET cc_start: 0.7522 (ttp) cc_final: 0.7241 (ttp) REVERT: A 859 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7319 (tpp80) REVERT: B 321 ASN cc_start: 0.8207 (t0) cc_final: 0.7863 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2147 time to fit residues: 47.8438 Evaluate side-chains 131 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 573 ASN A 782 HIS A 876 HIS ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7335 Z= 0.439 Angle : 0.726 7.184 10058 Z= 0.375 Chirality : 0.048 0.249 1164 Planarity : 0.004 0.033 1158 Dihedral : 15.705 178.389 1288 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.58 % Allowed : 13.30 % Favored : 83.12 % 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: -0.02 (0.29), residues: 805 helix: 0.91 (0.29), residues: 303 sheet: -0.35 (0.44), residues: 153 loop : -0.58 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 512 HIS 0.008 0.001 HIS B 260 PHE 0.019 0.002 PHE A 911 TYR 0.022 0.002 TYR A 303 ARG 0.004 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.787 Fit side-chains REVERT: A 241 PHE cc_start: 0.7985 (m-80) cc_final: 0.7748 (m-80) REVERT: A 283 LYS cc_start: 0.8460 (tppt) cc_final: 0.8154 (ttpt) REVERT: A 387 MET cc_start: 0.8938 (mmt) cc_final: 0.8705 (mmt) REVERT: A 481 ASP cc_start: 0.8158 (m-30) cc_final: 0.7885 (m-30) REVERT: A 610 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7387 (mtpp) REVERT: A 692 ASN cc_start: 0.8360 (m-40) cc_final: 0.7577 (t0) REVERT: A 756 TYR cc_start: 0.7532 (t80) cc_final: 0.7298 (t80) REVERT: A 761 MET cc_start: 0.7482 (ttp) cc_final: 0.7161 (ttp) REVERT: A 822 ASP cc_start: 0.8503 (m-30) cc_final: 0.7717 (t0) REVERT: A 879 TYR cc_start: 0.6678 (t80) cc_final: 0.6465 (t80) REVERT: B 321 ASN cc_start: 0.8186 (t0) cc_final: 0.7883 (t0) outliers start: 25 outliers final: 18 residues processed: 150 average time/residue: 0.1855 time to fit residues: 37.3697 Evaluate side-chains 144 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 271 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN A 876 HIS B 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7335 Z= 0.256 Angle : 0.605 6.514 10058 Z= 0.312 Chirality : 0.043 0.231 1164 Planarity : 0.003 0.034 1158 Dihedral : 15.484 178.812 1286 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.15 % Allowed : 18.88 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 805 helix: 1.32 (0.30), residues: 301 sheet: -0.19 (0.45), residues: 142 loop : -0.59 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 512 HIS 0.006 0.001 HIS B 260 PHE 0.014 0.001 PHE A 911 TYR 0.031 0.002 TYR A 541 ARG 0.002 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 0.844 Fit side-chains REVERT: A 241 PHE cc_start: 0.7938 (m-80) cc_final: 0.7697 (m-80) REVERT: A 244 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.7765 (mtt-85) REVERT: A 283 LYS cc_start: 0.8381 (tppt) cc_final: 0.8137 (ttpt) REVERT: A 387 MET cc_start: 0.8877 (mmt) cc_final: 0.8584 (mmt) REVERT: A 610 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7284 (mtpp) REVERT: A 625 ASN cc_start: 0.8338 (t0) cc_final: 0.8097 (t0) REVERT: A 692 ASN cc_start: 0.8451 (m-40) cc_final: 0.7680 (t0) REVERT: A 756 TYR cc_start: 0.7479 (t80) cc_final: 0.7213 (t80) REVERT: A 761 MET cc_start: 0.7392 (ttp) cc_final: 0.7039 (ttp) REVERT: A 822 ASP cc_start: 0.8396 (m-30) cc_final: 0.7597 (t0) REVERT: B 321 ASN cc_start: 0.8059 (t0) cc_final: 0.7784 (t0) REVERT: B 362 MET cc_start: 0.7778 (mmm) cc_final: 0.7553 (ttm) outliers start: 22 outliers final: 18 residues processed: 146 average time/residue: 0.2048 time to fit residues: 39.4303 Evaluate side-chains 147 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 678 GLN A 782 HIS A 876 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7335 Z= 0.357 Angle : 0.640 7.366 10058 Z= 0.329 Chirality : 0.045 0.246 1164 Planarity : 0.004 0.035 1158 Dihedral : 15.488 178.125 1286 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.86 % Allowed : 21.32 % Favored : 73.82 % 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: 0.08 (0.29), residues: 805 helix: 1.17 (0.29), residues: 303 sheet: -0.34 (0.43), residues: 151 loop : -0.69 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.007 0.001 HIS A 782 PHE 0.014 0.002 PHE A 911 TYR 0.019 0.002 TYR A 303 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.725 Fit side-chains REVERT: A 283 LYS cc_start: 0.8358 (tppt) cc_final: 0.8115 (ttpt) REVERT: A 610 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7440 (mtpp) REVERT: A 625 ASN cc_start: 0.8367 (t0) cc_final: 0.8082 (t0) REVERT: A 756 TYR cc_start: 0.7506 (t80) cc_final: 0.7248 (t80) REVERT: A 822 ASP cc_start: 0.8411 (m-30) cc_final: 0.7639 (t0) REVERT: B 321 ASN cc_start: 0.8128 (t0) cc_final: 0.7846 (t0) REVERT: B 362 MET cc_start: 0.7940 (mmm) cc_final: 0.7715 (tpp) outliers start: 34 outliers final: 29 residues processed: 147 average time/residue: 0.1628 time to fit residues: 32.9553 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 0.0000 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 HIS A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.004 0.028 7335 Z= 0.245 Angle : 0.587 6.684 10058 Z= 0.299 Chirality : 0.043 0.227 1164 Planarity : 0.003 0.035 1158 Dihedral : 15.428 176.630 1286 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.58 % Allowed : 22.46 % Favored : 72.96 % 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: 0.28 (0.30), residues: 805 helix: 1.43 (0.30), residues: 301 sheet: -0.13 (0.45), residues: 140 loop : -0.70 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 512 HIS 0.007 0.001 HIS A 782 PHE 0.012 0.001 PHE B 414 TYR 0.016 0.002 TYR A 303 ARG 0.002 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.772 Fit side-chains REVERT: A 244 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.7480 (mtm-85) REVERT: A 283 LYS cc_start: 0.8338 (tppt) cc_final: 0.8122 (ttpt) REVERT: A 541 TYR cc_start: 0.7643 (m-80) cc_final: 0.7416 (m-80) REVERT: A 610 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7374 (mtpp) REVERT: A 625 ASN cc_start: 0.8386 (t0) cc_final: 0.8107 (t0) REVERT: A 657 LYS cc_start: 0.8441 (tptp) cc_final: 0.7812 (tppt) REVERT: A 756 TYR cc_start: 0.7493 (t80) cc_final: 0.7206 (t80) REVERT: A 822 ASP cc_start: 0.8367 (m-30) cc_final: 0.7628 (t0) REVERT: B 321 ASN cc_start: 0.8100 (t0) cc_final: 0.7846 (t0) REVERT: B 362 MET cc_start: 0.7865 (mmm) cc_final: 0.7656 (tpp) outliers start: 32 outliers final: 26 residues processed: 150 average time/residue: 0.1833 time to fit residues: 37.3610 Evaluate side-chains 153 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 782 HIS A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7335 Z= 0.180 Angle : 0.546 6.240 10058 Z= 0.278 Chirality : 0.042 0.223 1164 Planarity : 0.003 0.035 1158 Dihedral : 15.390 174.925 1286 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.58 % Allowed : 22.75 % Favored : 72.68 % 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: 0.57 (0.30), residues: 805 helix: 1.66 (0.30), residues: 301 sheet: -0.08 (0.44), residues: 151 loop : -0.48 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 315 HIS 0.010 0.001 HIS A 876 PHE 0.009 0.001 PHE A 911 TYR 0.017 0.001 TYR A 390 ARG 0.002 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.782 Fit side-chains REVERT: A 244 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8188 (mtt-85) REVERT: A 283 LYS cc_start: 0.8304 (tppt) cc_final: 0.8098 (ttpt) REVERT: A 610 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7255 (mtpp) REVERT: A 657 LYS cc_start: 0.8420 (tptp) cc_final: 0.7786 (tppt) REVERT: A 756 TYR cc_start: 0.7479 (t80) cc_final: 0.7161 (t80) REVERT: A 822 ASP cc_start: 0.8408 (m-30) cc_final: 0.7514 (t0) REVERT: B 321 ASN cc_start: 0.8079 (t0) cc_final: 0.7875 (t0) REVERT: B 362 MET cc_start: 0.7803 (mmm) cc_final: 0.7595 (tpp) outliers start: 32 outliers final: 27 residues processed: 153 average time/residue: 0.1658 time to fit residues: 34.9455 Evaluate side-chains 153 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 0.0170 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- 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: 0.7491 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7335 Z= 0.153 Angle : 0.526 6.048 10058 Z= 0.267 Chirality : 0.041 0.220 1164 Planarity : 0.003 0.035 1158 Dihedral : 15.359 173.732 1286 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.29 % Allowed : 23.75 % Favored : 71.96 % 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: 0.72 (0.30), residues: 805 helix: 1.81 (0.30), residues: 301 sheet: 0.10 (0.44), residues: 150 loop : -0.47 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 315 HIS 0.003 0.001 HIS B 260 PHE 0.013 0.001 PHE B 414 TYR 0.017 0.001 TYR A 390 ARG 0.001 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.737 Fit side-chains REVERT: A 244 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8193 (mtt-85) REVERT: A 632 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7769 (tt) REVERT: A 657 LYS cc_start: 0.8397 (tptp) cc_final: 0.7769 (tppt) REVERT: A 756 TYR cc_start: 0.7512 (t80) cc_final: 0.7106 (t80) REVERT: A 822 ASP cc_start: 0.8346 (m-30) cc_final: 0.7503 (t0) REVERT: B 297 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: B 362 MET cc_start: 0.7789 (mmm) cc_final: 0.7579 (tpp) outliers start: 30 outliers final: 23 residues processed: 150 average time/residue: 0.1777 time to fit residues: 36.5537 Evaluate side-chains 150 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7335 Z= 0.394 Angle : 0.649 7.761 10058 Z= 0.334 Chirality : 0.045 0.259 1164 Planarity : 0.004 0.036 1158 Dihedral : 15.422 176.238 1286 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.58 % Allowed : 22.75 % Favored : 71.67 % 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 (0.30), residues: 805 helix: 1.40 (0.29), residues: 302 sheet: -0.17 (0.44), residues: 151 loop : -0.66 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 379 HIS 0.005 0.001 HIS B 260 PHE 0.012 0.002 PHE A 911 TYR 0.025 0.002 TYR A 541 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 0.737 Fit side-chains REVERT: A 504 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: A 610 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7576 (mtpp) REVERT: A 612 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 625 ASN cc_start: 0.8365 (t0) cc_final: 0.8057 (t0) REVERT: A 657 LYS cc_start: 0.8449 (tptp) cc_final: 0.7804 (tppt) REVERT: A 756 TYR cc_start: 0.7508 (t80) cc_final: 0.7167 (t80) REVERT: A 822 ASP cc_start: 0.8396 (m-30) cc_final: 0.7577 (t0) REVERT: B 297 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7189 (m-80) outliers start: 39 outliers final: 31 residues processed: 153 average time/residue: 0.1670 time to fit residues: 35.4782 Evaluate side-chains 155 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7335 Z= 0.173 Angle : 0.567 9.078 10058 Z= 0.284 Chirality : 0.042 0.222 1164 Planarity : 0.003 0.036 1158 Dihedral : 15.331 174.160 1286 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.15 % Allowed : 24.75 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 805 helix: 1.68 (0.30), residues: 301 sheet: 0.02 (0.44), residues: 151 loop : -0.53 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 315 HIS 0.003 0.001 HIS B 260 PHE 0.010 0.001 PHE A 911 TYR 0.027 0.002 TYR A 541 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.729 Fit side-chains REVERT: A 244 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8139 (mtt-85) REVERT: A 610 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7323 (mttm) REVERT: A 612 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 625 ASN cc_start: 0.8446 (t0) cc_final: 0.8141 (t0) REVERT: A 657 LYS cc_start: 0.8382 (tptp) cc_final: 0.7754 (tppt) REVERT: A 756 TYR cc_start: 0.7485 (t80) cc_final: 0.7103 (t80) REVERT: A 822 ASP cc_start: 0.8304 (m-30) cc_final: 0.7538 (t0) REVERT: B 297 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7016 (m-80) outliers start: 29 outliers final: 25 residues processed: 145 average time/residue: 0.1719 time to fit residues: 34.3426 Evaluate side-chains 152 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 6 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS A 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7335 Z= 0.120 Angle : 0.540 9.258 10058 Z= 0.266 Chirality : 0.040 0.216 1164 Planarity : 0.003 0.035 1158 Dihedral : 15.303 172.111 1286 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.29 % Allowed : 27.18 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 805 helix: 1.92 (0.30), residues: 301 sheet: 0.18 (0.44), residues: 150 loop : -0.43 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 315 HIS 0.003 0.001 HIS A 786 PHE 0.014 0.001 PHE B 414 TYR 0.028 0.002 TYR A 541 ARG 0.002 0.000 ARG B 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.810 Fit side-chains REVERT: A 625 ASN cc_start: 0.8397 (t0) cc_final: 0.8125 (t0) REVERT: A 632 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 657 LYS cc_start: 0.8323 (tptp) cc_final: 0.8098 (mmtm) REVERT: A 822 ASP cc_start: 0.8272 (m-30) cc_final: 0.7981 (t0) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.1819 time to fit residues: 34.4791 Evaluate side-chains 141 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 678 GLN ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.161575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.126800 restraints weight = 8077.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.127825 restraints weight = 7493.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129284 restraints weight = 6535.115| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7335 Z= 0.190 Angle : 0.563 8.596 10058 Z= 0.278 Chirality : 0.041 0.220 1164 Planarity : 0.003 0.035 1158 Dihedral : 15.280 172.805 1286 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.86 % Allowed : 28.18 % Favored : 69.96 % 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: 0.83 (0.30), residues: 805 helix: 1.96 (0.30), residues: 300 sheet: 0.17 (0.44), residues: 151 loop : -0.48 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.004 0.001 HIS A 544 PHE 0.010 0.001 PHE A 911 TYR 0.028 0.002 TYR A 541 ARG 0.002 0.000 ARG A 559 =============================================================================== Job complete usr+sys time: 1532.77 seconds wall clock time: 28 minutes 43.60 seconds (1723.60 seconds total)