Starting phenix.real_space_refine on Fri Dec 8 00:08:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/12_2023/7to2_26027_updated.pdb" } resolution = 3.2 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= 0.004 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 Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3733 2.51 5 N 1039 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5384 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 25, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 639 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 40.487 21.767 28.769 1.00 38.49 S ATOM 4596 SG CYS A 813 39.020 18.506 27.949 1.00 48.41 S ATOM 4908 SG CYS A 864 40.109 19.526 24.622 1.00 65.65 S ATOM 4947 SG CYS A 869 37.263 21.217 26.585 1.00 66.55 S Time building chain proxies: 4.03, per 1000 atoms: 0.67 Number of scatterers: 6052 At special positions: 0 Unit cell: (87.15, 97.65, 72.45, 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) Zn 1 29.99 S 33 16.00 P 32 15.00 Mg 1 11.99 O 1213 8.00 N 1039 7.00 C 3733 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " Number of angles added : 6 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 5 sheets defined 43.4% alpha, 8.4% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 334 through 340 removed outlier: 4.419A pdb=" N VAL A 338 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU A 339 " --> pdb=" O GLN A 336 " (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 394 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 520 Processing helix chain 'A' and resid 528 through 555 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.873A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 removed outlier: 3.883A pdb=" N SER A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 removed outlier: 3.711A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 836 through 841' 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 404 through 408 Processing sheet with id= B, first strand: chain 'A' and resid 457 through 462 Processing sheet with id= C, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.771A pdb=" N ILE A 693 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU A 661 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 695 " --> pdb=" O LEU A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 892 through 896 removed outlier: 3.692A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.968A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.65 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: 1473 1.33 - 1.45: 1254 1.45 - 1.57: 3397 1.57 - 1.70: 61 1.70 - 1.82: 46 Bond restraints: 6231 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.25e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.485 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N VAL A 699 " pdb=" CA VAL A 699 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.18e-02 7.18e+03 9.11e+00 ... (remaining 6226 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.74: 316 106.74 - 113.60: 3493 113.60 - 120.46: 2586 120.46 - 127.32: 2061 127.32 - 134.18: 94 Bond angle restraints: 8550 Sorted by residual: angle pdb=" C PRO A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta sigma weight residual 121.65 124.64 -2.99 6.80e-01 2.16e+00 1.93e+01 angle pdb=" C2' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " ideal model delta sigma weight residual 112.00 116.55 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N1 ADP A1003 " pdb=" C2 ADP A1003 " pdb=" N3 ADP A1003 " ideal model delta sigma weight residual 120.00 129.09 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.27e+00 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 120.70 117.78 2.92 1.03e+00 9.43e-01 8.03e+00 ... (remaining 8545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3411 16.18 - 32.37: 271 32.37 - 48.55: 73 48.55 - 64.73: 45 64.73 - 80.91: 19 Dihedral angle restraints: 3819 sinusoidal: 1854 harmonic: 1965 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -7.40 -52.60 1 2.00e+01 2.50e-03 9.42e+00 dihedral pdb=" CA LEU A 430 " pdb=" CB LEU A 430 " pdb=" CG LEU A 430 " pdb=" CD1 LEU A 430 " ideal model delta sinusoidal sigma weight residual 180.00 124.30 55.70 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " pdb=" CG ASP A 562 " pdb=" OD1 ASP A 562 " ideal model delta sinusoidal sigma weight residual -30.00 -81.64 51.64 1 2.00e+01 2.50e-03 9.11e+00 ... (remaining 3816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 427 0.043 - 0.085: 294 0.085 - 0.128: 224 0.128 - 0.171: 32 0.171 - 0.213: 2 Chirality restraints: 979 Sorted by residual: chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" P G B 45 " pdb=" OP1 G B 45 " pdb=" OP2 G B 45 " pdb=" O5' G B 45 " both_signs ideal model delta sigma weight residual True 2.41 -2.25 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 976 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 10 " -0.026 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 10 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G B 10 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 10 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 10 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 10 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 490 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C CYS A 490 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 490 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 491 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1003 " 0.011 2.00e-02 2.50e+03 9.35e-03 2.40e+00 pdb=" C2 ADP A1003 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ADP A1003 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ADP A1003 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP A1003 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N6 ADP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N7 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" N9 ADP A1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1192 2.81 - 3.33: 5969 3.33 - 3.85: 10248 3.85 - 4.38: 11747 4.38 - 4.90: 19777 Nonbonded interactions: 48933 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.284 2.520 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.296 2.440 nonbonded pdb=" O THR A 662 " pdb=" NE2 GLN A 678 " model vdw 2.334 2.520 nonbonded pdb=" O ASP A 690 " pdb=" ND1 HIS A 691 " model vdw 2.348 2.520 nonbonded pdb=" O SER A 698 " pdb=" OG SER A 698 " model vdw 2.353 2.440 ... (remaining 48928 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=1.00 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: 0.390 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: 0.020 Extract box with map and model: 1.860 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 0.096 6231 Z= 0.690 Angle : 1.131 9.092 8550 Z= 0.827 Chirality : 0.069 0.213 979 Planarity : 0.004 0.016 979 Dihedral : 15.192 80.913 2543 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 6.86 % Favored : 92.31 % 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: -1.96 (0.30), residues: 666 helix: 0.75 (0.28), residues: 298 sheet: -3.26 (0.49), residues: 75 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 771 HIS 0.005 0.001 HIS A 782 PHE 0.011 0.003 PHE A 460 TYR 0.012 0.003 TYR A 548 ARG 0.008 0.001 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.682 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2043 time to fit residues: 25.0866 Evaluate side-chains 59 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0632 time to fit residues: 1.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 375 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN A 477 GLN A 500 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.175 Angle : 0.476 6.670 8550 Z= 0.230 Chirality : 0.038 0.136 979 Planarity : 0.002 0.023 979 Dihedral : 14.221 80.956 1172 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.34 % Allowed : 13.21 % Favored : 85.45 % 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: -0.77 (0.32), residues: 666 helix: 1.94 (0.30), residues: 299 sheet: -3.04 (0.50), residues: 76 loop : -2.57 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.006 0.001 PHE A 295 TYR 0.007 0.001 TYR A 246 ARG 0.005 0.000 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.704 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1658 time to fit residues: 16.5301 Evaluate side-chains 57 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0659 time to fit residues: 1.2670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.186 Angle : 0.479 5.644 8550 Z= 0.232 Chirality : 0.038 0.133 979 Planarity : 0.003 0.025 979 Dihedral : 14.197 82.960 1172 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.01 % Allowed : 14.38 % Favored : 83.61 % 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 (0.33), residues: 666 helix: 2.30 (0.30), residues: 299 sheet: -2.66 (0.57), residues: 64 loop : -2.25 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.005 0.001 PHE A 295 TYR 0.007 0.001 TYR A 566 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.591 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 73 average time/residue: 0.1360 time to fit residues: 14.8604 Evaluate side-chains 60 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0728 time to fit residues: 1.2716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6231 Z= 0.258 Angle : 0.507 5.667 8550 Z= 0.249 Chirality : 0.039 0.145 979 Planarity : 0.003 0.027 979 Dihedral : 14.228 83.870 1172 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.84 % Allowed : 16.05 % Favored : 82.11 % 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 (0.33), residues: 666 helix: 2.33 (0.30), residues: 300 sheet: -2.53 (0.59), residues: 64 loop : -2.12 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.001 HIS A 280 PHE 0.006 0.001 PHE A 295 TYR 0.010 0.001 TYR A 473 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.701 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 71 average time/residue: 0.1577 time to fit residues: 16.5970 Evaluate side-chains 59 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0671 time to fit residues: 1.2660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.203 Angle : 0.506 5.631 8550 Z= 0.248 Chirality : 0.038 0.137 979 Planarity : 0.003 0.029 979 Dihedral : 14.228 84.717 1172 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.00 % Allowed : 17.39 % Favored : 81.61 % 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: 0.06 (0.33), residues: 666 helix: 2.45 (0.30), residues: 301 sheet: -2.42 (0.60), residues: 64 loop : -2.04 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.005 0.001 PHE A 295 TYR 0.012 0.001 TYR A 473 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.633 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 0.1334 time to fit residues: 13.1323 Evaluate side-chains 58 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0613 time to fit residues: 1.2149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6231 Z= 0.135 Angle : 0.473 5.665 8550 Z= 0.231 Chirality : 0.037 0.139 979 Planarity : 0.003 0.030 979 Dihedral : 14.230 85.743 1172 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.00 % Allowed : 18.23 % Favored : 80.77 % 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 (0.34), residues: 666 helix: 2.65 (0.30), residues: 301 sheet: -2.31 (0.61), residues: 64 loop : -1.95 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.005 0.001 PHE A 371 TYR 0.011 0.001 TYR A 473 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.725 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.1323 time to fit residues: 12.4517 Evaluate side-chains 60 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0712 time to fit residues: 1.4070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6231 Z= 0.251 Angle : 0.531 6.281 8550 Z= 0.262 Chirality : 0.039 0.158 979 Planarity : 0.003 0.029 979 Dihedral : 14.250 85.158 1172 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.84 % Allowed : 18.23 % Favored : 80.94 % 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: 0.26 (0.33), residues: 666 helix: 2.58 (0.30), residues: 301 sheet: -2.28 (0.62), residues: 64 loop : -1.90 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.001 HIS A 280 PHE 0.007 0.001 PHE A 295 TYR 0.012 0.001 TYR A 473 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.616 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 60 average time/residue: 0.1484 time to fit residues: 13.3092 Evaluate side-chains 55 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6231 Z= 0.151 Angle : 0.485 6.659 8550 Z= 0.238 Chirality : 0.038 0.159 979 Planarity : 0.003 0.029 979 Dihedral : 14.248 86.038 1172 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.17 % Allowed : 18.23 % Favored : 80.60 % 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: 0.42 (0.34), residues: 666 helix: 2.72 (0.30), residues: 301 sheet: -2.21 (0.62), residues: 64 loop : -1.83 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.006 0.001 PHE A 471 TYR 0.015 0.001 TYR A 473 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.687 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.1553 time to fit residues: 13.6878 Evaluate side-chains 58 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1670 time to fit residues: 1.8089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6231 Z= 0.165 Angle : 0.492 7.218 8550 Z= 0.240 Chirality : 0.038 0.197 979 Planarity : 0.003 0.030 979 Dihedral : 14.239 85.974 1172 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.50 % Allowed : 18.23 % Favored : 81.27 % 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: 0.47 (0.34), residues: 666 helix: 2.74 (0.29), residues: 301 sheet: -2.11 (0.63), residues: 64 loop : -1.79 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.005 0.001 PHE A 471 TYR 0.014 0.001 TYR A 473 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.670 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.1333 time to fit residues: 11.4317 Evaluate side-chains 55 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0717 time to fit residues: 1.1500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6231 Z= 0.335 Angle : 0.567 7.385 8550 Z= 0.279 Chirality : 0.041 0.204 979 Planarity : 0.003 0.032 979 Dihedral : 14.303 84.567 1172 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.17 % Allowed : 18.56 % Favored : 81.27 % 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 (0.33), residues: 666 helix: 2.49 (0.30), residues: 302 sheet: -2.10 (0.63), residues: 64 loop : -1.84 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 771 HIS 0.002 0.001 HIS A 280 PHE 0.007 0.001 PHE A 295 TYR 0.018 0.001 TYR A 473 ARG 0.002 0.000 ARG A 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.712 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1490 time to fit residues: 10.9311 Evaluate side-chains 49 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0816 time to fit residues: 1.0950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092066 restraints weight = 8126.792| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.28 r_work: 0.2957 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 0.032 6231 Z= 0.161 Angle : 0.507 7.512 8550 Z= 0.250 Chirality : 0.038 0.193 979 Planarity : 0.003 0.033 979 Dihedral : 14.263 85.908 1172 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.33 % Allowed : 18.73 % Favored : 80.94 % 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 (0.33), residues: 666 helix: 2.66 (0.30), residues: 301 sheet: -2.07 (0.63), residues: 64 loop : -1.76 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.005 0.001 PHE A 633 TYR 0.015 0.001 TYR A 473 ARG 0.002 0.000 ARG A 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.61 seconds wall clock time: 27 minutes 56.41 seconds (1676.41 seconds total)