Starting phenix.real_space_refine (version: dev) on Mon Apr 4 17:30:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n73_24218/04_2022/7n73_24218_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7866 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 7866 Unusual residues: {'ALF': 1, ' MG': 2, 'Y01': 2, 'ADP': 1} Classifications: {'undetermined': 6, 'water': 3, 'peptide': 1036} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 69, 'TRANS': 963, None: 9, 'PCIS': 3} Not linked: pdbres="PRO A1168 " pdbres="ADP A1201 " Not linked: pdbres="ADP A1201 " pdbres="ALF A1202 " Not linked: pdbres="ALF A1202 " pdbres=" MG A1203 " Not linked: pdbres=" MG A1203 " pdbres=" MG A1204 " Not linked: pdbres=" MG A1204 " pdbres="Y01 A1205 " ... (remaining 4 not shown) Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 4.87, per 1000 atoms: 0.62 Number of scatterers: 7866 At special positions: 0 Unit cell: (92.312, 99.655, 125.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 49 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1398 8.00 N 1322 7.00 C 5088 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 10 sheets defined 47.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 197 removed outlier: 4.708A pdb=" N HIS A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.778A pdb=" N ALA A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 252 through 283 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 420 through 444 removed outlier: 3.848A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.722A pdb=" N ILE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 Processing helix chain 'A' and resid 493 through 501 removed outlier: 3.617A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 567 through 576 removed outlier: 3.608A pdb=" N THR A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.965A pdb=" N GLN A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 725 through 736 Proline residue: A 729 - end of helix Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 822 through 831 Processing helix chain 'A' and resid 833 through 842 Proline residue: A 837 - end of helix removed outlier: 3.665A pdb=" N GLN A 842 " --> pdb=" O LYS A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 864 removed outlier: 3.626A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 4.921A pdb=" N GLY A 879 " --> pdb=" O ASN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 949 Proline residue: A 912 - end of helix removed outlier: 3.648A pdb=" N LEU A 937 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 938 " --> pdb=" O TYR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 3.761A pdb=" N LEU A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 removed outlier: 4.361A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1020 removed outlier: 3.647A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1060 removed outlier: 3.875A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1074 through 1092 Processing helix chain 'A' and resid 1109 through 1144 removed outlier: 3.629A pdb=" N PHE A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1153 through 1163 Processing sheet with id= A, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.538A pdb=" N ILE A 169 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 178 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 289 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.522A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.559A pdb=" N ASN A 336 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE A 375 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 488 through 490 Processing sheet with id= G, first strand: chain 'A' and resid 740 through 743 removed outlier: 6.219A pdb=" N VAL A 886 " --> pdb=" O MET A 870 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 588 through 590 removed outlier: 4.127A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.021A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 522 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 783 through 788 removed outlier: 7.686A pdb=" N LEU A 820 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 846 " --> pdb=" O LEU A 820 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 3.70 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: 2157 1.33 - 1.45: 1155 1.45 - 1.57: 4636 1.57 - 1.69: 11 1.69 - 1.81: 77 Bond restraints: 8036 Sorted by residual: bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.808 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.788 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" CAV Y01 A1205 " pdb=" CBC Y01 A1205 " ideal model delta sigma weight residual 1.523 1.605 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 8031 not shown) Histogram of bond angle deviations from ideal: 89.25 - 107.31: 412 107.31 - 125.38: 10446 125.38 - 143.45: 131 143.45 - 161.52: 0 161.52 - 179.59: 2 Bond angle restraints: 10991 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.71 -70.03 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.59 -69.96 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 89.87 20.34 3.00e+00 1.11e-01 4.60e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 89.25 19.77 3.00e+00 1.11e-01 4.34e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 90.35 19.34 3.00e+00 1.11e-01 4.15e+01 ... (remaining 10986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 4571 22.30 - 44.60: 215 44.60 - 66.89: 20 66.89 - 89.19: 4 89.19 - 111.49: 2 Dihedral angle restraints: 4812 sinusoidal: 1818 harmonic: 2994 Sorted by residual: dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -171.49 111.49 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 50.14 -110.14 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -125.53 65.53 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 4809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1328 0.231 - 0.462: 6 0.462 - 0.692: 0 0.692 - 0.923: 0 0.923 - 1.154: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 617 " pdb=" CA VAL A 617 " pdb=" CG1 VAL A 617 " pdb=" CG2 VAL A 617 " both_signs ideal model delta sigma weight residual False -2.63 -1.48 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CBG Y01 A1205 " pdb=" CAQ Y01 A1205 " pdb=" CBD Y01 A1205 " pdb=" CBI Y01 A1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBG Y01 A1206 " pdb=" CAQ Y01 A1206 " pdb=" CBD Y01 A1206 " pdb=" CBI Y01 A1206 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1332 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 174 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" CD GLN A 174 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN A 174 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 174 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 451 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" CD GLU A 451 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 451 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 451 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 590 " -0.018 2.00e-02 2.50e+03 1.68e-02 4.96e+00 pdb=" CG PHE A 590 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 590 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 590 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 590 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 590 " -0.006 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 50 2.46 - 3.07: 5672 3.07 - 3.68: 12033 3.68 - 4.29: 17769 4.29 - 4.90: 30606 Nonbonded interactions: 66130 Sorted by model distance: nonbonded pdb=" O THR A 510 " pdb="MG MG A1203 " model vdw 1.850 2.170 nonbonded pdb=" NZ LYS A1062 " pdb=" OD2 ASP A1134 " model vdw 2.043 2.520 nonbonded pdb=" O LEU A 672 " pdb=" OG1 THR A 676 " model vdw 2.062 2.440 nonbonded pdb=" O VAL A 462 " pdb=" O HOH A1301 " model vdw 2.066 2.440 nonbonded pdb=" OG1 THR A 745 " pdb=" F1 ALF A1202 " model vdw 2.070 2.390 ... (remaining 66125 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5088 2.51 5 N 1322 2.21 5 O 1398 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 25.730 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 8036 Z= 0.387 Angle : 1.268 70.028 10991 Z= 0.490 Chirality : 0.064 1.154 1335 Planarity : 0.004 0.032 1373 Dihedral : 13.017 111.491 2878 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.31 (0.27), residues: 1024 helix: 1.63 (0.24), residues: 500 sheet: -0.24 (0.42), residues: 158 loop : 0.51 (0.35), residues: 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.951 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 1.1159 time to fit residues: 71.0351 Evaluate side-chains 37 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8036 Z= 0.199 Angle : 0.857 29.827 10991 Z= 0.348 Chirality : 0.041 0.146 1335 Planarity : 0.005 0.037 1373 Dihedral : 6.945 96.830 1146 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.50 (0.27), residues: 1024 helix: 1.70 (0.24), residues: 495 sheet: -0.16 (0.42), residues: 155 loop : 0.75 (0.35), residues: 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.0776 time to fit residues: 56.3222 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 78 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8487 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8036 Z= 0.160 Angle : 0.822 30.176 10991 Z= 0.327 Chirality : 0.040 0.141 1335 Planarity : 0.005 0.037 1373 Dihedral : 6.493 91.827 1146 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.60 (0.27), residues: 1024 helix: 1.81 (0.24), residues: 490 sheet: 0.02 (0.43), residues: 152 loop : 0.70 (0.34), residues: 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 48 average time/residue: 1.0852 time to fit residues: 56.7924 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.0778 time to fit residues: 2.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8036 Z= 0.190 Angle : 0.824 30.028 10991 Z= 0.326 Chirality : 0.040 0.141 1335 Planarity : 0.005 0.039 1373 Dihedral : 6.178 93.515 1146 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.60 (0.27), residues: 1024 helix: 1.80 (0.24), residues: 491 sheet: 0.10 (0.43), residues: 147 loop : 0.66 (0.33), residues: 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 1.191 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 1.0358 time to fit residues: 52.2858 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 8036 Z= 0.291 Angle : 0.845 30.325 10991 Z= 0.339 Chirality : 0.041 0.141 1335 Planarity : 0.005 0.038 1373 Dihedral : 6.213 99.482 1146 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.51 (0.27), residues: 1024 helix: 1.71 (0.24), residues: 488 sheet: 0.00 (0.42), residues: 152 loop : 0.68 (0.33), residues: 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.959 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 51 average time/residue: 0.9494 time to fit residues: 53.1213 Evaluate side-chains 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1946 time to fit residues: 2.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 8036 Z= 0.228 Angle : 0.836 30.144 10991 Z= 0.332 Chirality : 0.040 0.140 1335 Planarity : 0.005 0.037 1373 Dihedral : 6.106 102.144 1146 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1024 helix: 1.71 (0.24), residues: 490 sheet: 0.00 (0.42), residues: 152 loop : 0.70 (0.33), residues: 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.881 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 0.9719 time to fit residues: 60.5864 Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0720 time to fit residues: 1.3491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 8036 Z= 0.238 Angle : 0.834 29.974 10991 Z= 0.333 Chirality : 0.041 0.140 1335 Planarity : 0.005 0.037 1373 Dihedral : 6.069 104.579 1146 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.54 (0.27), residues: 1024 helix: 1.71 (0.24), residues: 490 sheet: 0.02 (0.42), residues: 152 loop : 0.73 (0.33), residues: 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.994 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 1.0314 time to fit residues: 57.5669 Evaluate side-chains 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.2504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 892 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 8036 Z= 0.169 Angle : 0.831 29.805 10991 Z= 0.327 Chirality : 0.040 0.139 1335 Planarity : 0.004 0.037 1373 Dihedral : 5.896 101.523 1146 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.61 (0.27), residues: 1024 helix: 1.78 (0.24), residues: 489 sheet: 0.09 (0.42), residues: 152 loop : 0.75 (0.33), residues: 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.922 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.9999 time to fit residues: 50.5754 Evaluate side-chains 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0827 time to fit residues: 1.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 8036 Z= 0.141 Angle : 0.810 29.814 10991 Z= 0.318 Chirality : 0.039 0.138 1335 Planarity : 0.004 0.036 1373 Dihedral : 5.570 93.048 1146 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.72 (0.27), residues: 1024 helix: 1.80 (0.24), residues: 500 sheet: 0.33 (0.43), residues: 147 loop : 0.77 (0.34), residues: 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.981 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.9107 time to fit residues: 49.2864 Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 8036 Z= 0.177 Angle : 0.828 29.726 10991 Z= 0.324 Chirality : 0.040 0.137 1335 Planarity : 0.004 0.039 1373 Dihedral : 5.589 94.481 1146 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.73 (0.27), residues: 1024 helix: 1.81 (0.24), residues: 501 sheet: 0.39 (0.44), residues: 147 loop : 0.74 (0.34), residues: 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.999 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.9686 time to fit residues: 51.2797 Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1122 ASN ** 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 = 0.3544 r_free = 0.3544 target = 0.091552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069819 restraints weight = 17216.385| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.69 r_work: 0.3121 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.3096 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work: 0.3084 rms_B_bonded: 2.53 restraints_weight: 0.0625 r_work: 0.3071 rms_B_bonded: 2.63 restraints_weight: 0.0312 r_work: 0.3058 rms_B_bonded: 2.74 restraints_weight: 0.0156 r_work: 0.3045 rms_B_bonded: 2.89 restraints_weight: 0.0078 r_work: 0.3031 rms_B_bonded: 3.06 restraints_weight: 0.0039 r_work: 0.3016 rms_B_bonded: 3.26 restraints_weight: 0.0020 r_work: 0.3000 rms_B_bonded: 3.48 restraints_weight: 0.0010 r_work: 0.2984 rms_B_bonded: 3.74 restraints_weight: 0.0005 r_work: 0.2967 rms_B_bonded: 4.02 restraints_weight: 0.0002 r_work: 0.2949 rms_B_bonded: 4.34 restraints_weight: 0.0001 r_work: 0.2930 rms_B_bonded: 4.70 restraints_weight: 0.0001 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 8036 Z= 0.158 Angle : 0.814 29.804 10991 Z= 0.319 Chirality : 0.039 0.138 1335 Planarity : 0.004 0.039 1373 Dihedral : 5.505 92.704 1146 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.76 (0.27), residues: 1024 helix: 1.84 (0.24), residues: 501 sheet: 0.38 (0.43), residues: 147 loop : 0.75 (0.34), residues: 376 =============================================================================== Job complete usr+sys time: 2068.34 seconds wall clock time: 38 minutes 12.82 seconds (2292.82 seconds total)