Starting phenix.real_space_refine (version: dev) on Mon Apr 4 16:27:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/04_2022/7n77_24222_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/04_2022/7n77_24222.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/7n77_24222/04_2022/7n77_24222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/04_2022/7n77_24222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/04_2022/7n77_24222_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/04_2022/7n77_24222_trim_updated.pdb" } resolution = 3.2 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= 0.023 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7470 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7470 Unusual residues: {'ALF': 1, ' MG': 1, 'Y01': 2} Classifications: {'undetermined': 4, 'water': 2, 'peptide': 1036} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 69, 'TRANS': 963, None: 6, 'PCIS': 3} Not linked: pdbres="PRO A1168 " pdbres="ALF A1201 " Not linked: pdbres="ALF A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="Y01 A1203 " Not linked: pdbres="Y01 A1203 " pdbres="Y01 A1204 " Not linked: pdbres="Y01 A1204 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 845 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 4, 'Y01:plan-2': 1, 'Y01:plan-1': 1, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 347 Time building chain proxies: 4.85, per 1000 atoms: 0.65 Number of scatterers: 7470 At special positions: 0 Unit cell: (91.43, 104.81, 130.455, 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) S 45 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1333 8.00 N 1281 7.00 C 4805 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: 3.14 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: 39 helices and 8 sheets defined 46.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' 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: 3.722A pdb=" N ARG A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N HIS A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.835A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 252 through 283 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.882A pdb=" N THR A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) 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: 4.472A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.804A pdb=" N ILE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 486 removed outlier: 3.741A pdb=" N GLN A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.940A 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: 3.751A 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 678 removed outlier: 3.667A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 4.078A 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 735 Proline residue: A 729 - end of helix Processing helix chain 'A' and resid 749 through 758 Processing helix chain 'A' and resid 822 through 831 Processing helix chain 'A' and resid 837 through 840 No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 851 through 864 removed outlier: 3.936A pdb=" N THR A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 883 removed outlier: 4.252A pdb=" N LEU A 881 " --> pdb=" O CYS A 878 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 882 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 948 Proline residue: A 912 - end of helix removed outlier: 4.352A pdb=" N ARG A 916 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 925 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 937 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 938 " --> pdb=" O TYR A 935 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 948 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 Processing helix chain 'A' and resid 966 through 975 removed outlier: 4.437A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1020 removed outlier: 4.077A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1060 removed outlier: 3.701A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.990A 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 1110 through 1144 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 88 through 92 removed outlier: 3.563A pdb=" N VAL A 105 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 92 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.567A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.507A pdb=" N VAL A 302 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.513A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.557A pdb=" N GLN A 377 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN A 336 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 375 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 740 through 743 Processing sheet with id= G, first strand: chain 'A' and resid 588 through 590 removed outlier: 4.230A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 635 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG A 622 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 783 through 788 removed outlier: 3.647A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 771 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 820 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 846 " --> pdb=" O LEU A 820 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 957 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: 2.67 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1197 1.31 - 1.43: 1857 1.43 - 1.56: 4476 1.56 - 1.68: 10 1.68 - 1.81: 71 Bond restraints: 7611 Sorted by residual: bond pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.780 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" F4 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C TYR A 935 " pdb=" O TYR A 935 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.29e-02 6.01e+03 1.74e+01 ... (remaining 7606 not shown) Histogram of bond angle deviations from ideal: 89.44 - 107.41: 347 107.41 - 125.39: 9962 125.39 - 143.37: 103 143.37 - 161.34: 0 161.34 - 179.32: 2 Bond angle restraints: 10414 Sorted by residual: angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F2 ALF A1201 " ideal model delta sigma weight residual 108.68 179.32 -70.64 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.63 178.41 -68.78 3.00e+00 1.11e-01 5.26e+02 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 110.21 89.91 20.30 3.00e+00 1.11e-01 4.58e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.69 89.44 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.02 90.03 18.99 3.00e+00 1.11e-01 4.01e+01 ... (remaining 10409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4187 17.37 - 34.73: 290 34.73 - 52.09: 48 52.09 - 69.46: 7 69.46 - 86.82: 6 Dihedral angle restraints: 4538 sinusoidal: 1545 harmonic: 2993 Sorted by residual: dihedral pdb=" CA PHE A 507 " pdb=" C PHE A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA A 85 " pdb=" C ALA A 85 " pdb=" N GLU A 86 " pdb=" CA GLU A 86 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA HIS A 492 " pdb=" C HIS A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta harmonic sigma weight residual -180.00 -163.27 -16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1154 0.086 - 0.172: 115 0.172 - 0.258: 5 0.258 - 0.343: 2 0.343 - 0.429: 5 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA TYR A 935 " pdb=" N TYR A 935 " pdb=" C TYR A 935 " pdb=" CB TYR A 935 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CBH Y01 A1204 " pdb=" CAT Y01 A1204 " pdb=" CAZ Y01 A1204 " pdb=" CBF Y01 A1204 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBG Y01 A1203 " pdb=" CAQ Y01 A1203 " pdb=" CBD Y01 A1203 " pdb=" CBI Y01 A1203 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 1278 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 856 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" CD GLU A 856 " -0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU A 856 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A 856 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 317 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" CD GLN A 317 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN A 317 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 317 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 894 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CD GLU A 894 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 894 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 894 " -0.014 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 10 2.33 - 2.98: 3706 2.98 - 3.62: 11042 3.62 - 4.26: 16433 4.26 - 4.90: 28429 Nonbonded interactions: 59620 Sorted by model distance: nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 1.692 2.170 nonbonded pdb=" F2 ALF A1201 " pdb="MG MG A1202 " model vdw 1.857 2.120 nonbonded pdb=" OE2 GLU A 110 " pdb=" OH TYR A 160 " model vdw 2.024 2.440 nonbonded pdb=" OD2 ASP A 508 " pdb=" F2 ALF A1201 " model vdw 2.116 2.390 nonbonded pdb=" OG SER A 889 " pdb=" OG SER A 899 " model vdw 2.189 2.440 ... (remaining 59615 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 45 5.16 5 C 4805 2.51 5 N 1281 2.21 5 O 1333 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.970 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 24.630 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 0.098 7611 Z= 0.406 Angle : 1.312 70.642 10414 Z= 0.526 Chirality : 0.056 0.429 1281 Planarity : 0.006 0.050 1320 Dihedral : 12.819 86.825 2604 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.14 % 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: -1.56 (0.24), residues: 1024 helix: -0.52 (0.22), residues: 482 sheet: -1.63 (0.37), residues: 178 loop : -1.15 (0.31), residues: 364 *********************** 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 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1607 time to fit residues: 12.5380 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1031 time to fit residues: 1.3747 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7611 Z= 0.194 Angle : 0.854 30.455 10414 Z= 0.346 Chirality : 0.041 0.191 1281 Planarity : 0.005 0.036 1320 Dihedral : 5.300 52.614 1122 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.56 % 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: 0.09 (0.26), residues: 1024 helix: 0.98 (0.24), residues: 482 sheet: -1.14 (0.39), residues: 164 loop : -0.43 (0.32), residues: 378 *********************** 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 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.855 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1423 time to fit residues: 9.8844 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0793 time to fit residues: 1.5802 ------------------------------------------------------------------------------- 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: 50.0000 chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7611 Z= 0.242 Angle : 0.848 30.817 10414 Z= 0.341 Chirality : 0.041 0.137 1281 Planarity : 0.004 0.037 1320 Dihedral : 5.163 57.445 1122 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.71 % 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: 0.57 (0.27), residues: 1024 helix: 1.36 (0.24), residues: 485 sheet: -1.14 (0.38), residues: 174 loop : 0.01 (0.35), residues: 365 *********************** 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 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.909 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.1410 time to fit residues: 10.2050 Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0702 time to fit residues: 1.3026 ------------------------------------------------------------------------------- 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: 0.2980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7611 Z= 0.188 Angle : 0.832 30.487 10414 Z= 0.329 Chirality : 0.040 0.126 1281 Planarity : 0.004 0.036 1320 Dihedral : 5.077 61.743 1122 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.85 % 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: 0.95 (0.27), residues: 1024 helix: 1.68 (0.25), residues: 481 sheet: -1.10 (0.37), residues: 174 loop : 0.28 (0.34), residues: 369 *********************** 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: 6 poor density : 41 time to evaluate : 0.870 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.1488 time to fit residues: 11.0588 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0782 time to fit residues: 1.6584 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 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: 0.7455 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.209 Angle : 0.843 30.750 10414 Z= 0.332 Chirality : 0.040 0.127 1281 Planarity : 0.004 0.036 1320 Dihedral : 4.920 64.117 1122 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.99 % 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: 1.01 (0.28), residues: 1024 helix: 1.69 (0.25), residues: 490 sheet: -1.06 (0.36), residues: 183 loop : 0.39 (0.35), residues: 351 *********************** 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 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.873 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1426 time to fit residues: 10.7460 Evaluate side-chains 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0709 time to fit residues: 1.8698 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 50.0000 chunk 97 optimal weight: 0.0570 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.185 Angle : 0.833 30.480 10414 Z= 0.326 Chirality : 0.040 0.128 1281 Planarity : 0.004 0.036 1320 Dihedral : 4.778 64.926 1122 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.71 % 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: 1.04 (0.27), residues: 1024 helix: 1.67 (0.24), residues: 502 sheet: -1.05 (0.37), residues: 180 loop : 0.42 (0.35), residues: 342 *********************** 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.905 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.1504 time to fit residues: 10.9760 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0839 time to fit residues: 1.4862 ------------------------------------------------------------------------------- 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: 6.9990 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 62 optimal weight: 0.0470 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 overall best weight: 1.0234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.193 Angle : 0.848 30.545 10414 Z= 0.331 Chirality : 0.040 0.126 1281 Planarity : 0.004 0.035 1320 Dihedral : 4.685 65.572 1122 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.71 % 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: 1.12 (0.27), residues: 1024 helix: 1.72 (0.24), residues: 504 sheet: -1.02 (0.36), residues: 185 loop : 0.50 (0.36), residues: 335 *********************** 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.954 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.1435 time to fit residues: 11.0094 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2545 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7611 Z= 0.143 Angle : 0.835 30.181 10414 Z= 0.324 Chirality : 0.039 0.127 1281 Planarity : 0.004 0.036 1320 Dihedral : 4.537 65.722 1122 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.28 % 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: 1.26 (0.27), residues: 1024 helix: 1.79 (0.24), residues: 504 sheet: -0.86 (0.37), residues: 180 loop : 0.55 (0.35), residues: 340 *********************** 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 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.893 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1518 time to fit residues: 11.0930 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2585 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7611 Z= 0.196 Angle : 0.860 30.623 10414 Z= 0.336 Chirality : 0.040 0.125 1281 Planarity : 0.004 0.035 1320 Dihedral : 4.540 66.175 1122 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.42 % 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: 1.27 (0.27), residues: 1024 helix: 1.80 (0.24), residues: 504 sheet: -0.85 (0.37), residues: 185 loop : 0.58 (0.36), residues: 335 *********************** 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 45 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.903 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.1526 time to fit residues: 11.3519 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0766 time to fit residues: 1.3251 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 50.0000 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7611 Z= 0.182 Angle : 0.853 30.409 10414 Z= 0.333 Chirality : 0.040 0.188 1281 Planarity : 0.004 0.035 1320 Dihedral : 4.500 66.199 1122 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.14 % 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: 1.34 (0.27), residues: 1024 helix: 1.85 (0.24), residues: 504 sheet: -0.79 (0.37), residues: 180 loop : 0.60 (0.35), residues: 340 ********************** 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 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.935 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.1529 time to fit residues: 10.5607 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0742 time to fit residues: 1.3986 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 59 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 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 = 0.3658 r_free = 0.3658 target = 0.078694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056076 restraints weight = 26046.233| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.70 r_work: 0.3060 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work: 0.3042 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work: 0.3033 rms_B_bonded: 3.49 restraints_weight: 0.0625 r_work: 0.3024 rms_B_bonded: 3.54 restraints_weight: 0.0312 r_work: 0.3014 rms_B_bonded: 3.60 restraints_weight: 0.0156 r_work: 0.3005 rms_B_bonded: 3.68 restraints_weight: 0.0078 r_work: 0.2995 rms_B_bonded: 3.77 restraints_weight: 0.0039 r_work: 0.2985 rms_B_bonded: 3.87 restraints_weight: 0.0020 r_work: 0.2975 rms_B_bonded: 3.99 restraints_weight: 0.0010 r_work: 0.2965 rms_B_bonded: 4.12 restraints_weight: 0.0005 r_work: 0.2954 rms_B_bonded: 4.26 restraints_weight: 0.0002 r_work: 0.2943 rms_B_bonded: 4.42 restraints_weight: 0.0001 r_work: 0.2932 rms_B_bonded: 4.59 restraints_weight: 0.0001 r_work: 0.2920 rms_B_bonded: 4.78 restraints_weight: 0.0000 r_work: 0.2908 rms_B_bonded: 4.98 restraints_weight: 0.0000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7611 Z= 0.229 Angle : 0.874 30.709 10414 Z= 0.343 Chirality : 0.041 0.188 1281 Planarity : 0.004 0.035 1320 Dihedral : 4.558 66.333 1122 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.28 % 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: 1.32 (0.27), residues: 1024 helix: 1.85 (0.24), residues: 504 sheet: -0.85 (0.37), residues: 185 loop : 0.60 (0.36), residues: 335 =============================================================================== Job complete usr+sys time: 1476.80 seconds wall clock time: 27 minutes 33.21 seconds (1653.21 seconds total)