Starting phenix.real_space_refine on Thu Jan 18 06:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/01_2024/7n78_24223_trim.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4971 2.51 5 N 1283 2.21 5 O 1366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7669 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 7669 Unusual residues: {' MG': 1, 'LMT': 3, 'PC1': 2, 'PO4': 1, 'SPM': 1, 'Y01': 3} Classifications: {'peptide': 1030, 'undetermined': 11, 'water': 3} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 958, None: 14} Not linked: pdbres="PRO A1168 " pdbres="PO4 A1201 " Not linked: pdbres="PO4 A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="SPM A1203 " Not linked: pdbres="SPM A1203 " pdbres="Y01 A1204 " Not linked: pdbres="Y01 A1204 " pdbres="Y01 A1205 " ... (remaining 9 not shown) Chain breaks: 6 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 661 Unresolved non-hydrogen angles: 860 Unresolved non-hydrogen dihedrals: 640 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 2, 'PC1:plan-2': 1, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 299 Time building chain proxies: 4.82, per 1000 atoms: 0.63 Number of scatterers: 7669 At special positions: 0 Unit cell: (81.079, 104.765, 133.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 2 15.00 Mg 1 11.99 O 1366 8.00 N 1283 7.00 C 4971 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 51.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.050A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.717A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 251 through 284 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 417 through 445 Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.937A pdb=" N VAL A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 4.458A pdb=" N CYS A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A 476 " --> pdb=" O MET A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.801A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.540A pdb=" N ARG A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.888A pdb=" N VAL A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.648A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.876A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.896A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 948 removed outlier: 3.683A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.756A pdb=" N THR A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.838A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1092 Processing helix chain 'A' and resid 1108 through 1145 removed outlier: 3.644A pdb=" N PHE A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.111A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.354A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.491A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.576A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 868 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.974A pdb=" N ALA A 530 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 527 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 714 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 443 hydrogen bonds defined for protein. 1266 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: 3.21 Time building geometry restraints manager: 3.54 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: 1596 1.33 - 1.45: 1554 1.45 - 1.57: 4583 1.57 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 7813 Sorted by residual: bond pdb=" C31 PC1 A1206 " pdb=" O31 PC1 A1206 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C21 PC1 A1206 " pdb=" O21 PC1 A1206 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C21 PC1 A1210 " pdb=" O21 PC1 A1210 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O1 PO4 A1201 " pdb=" P PO4 A1201 " ideal model delta sigma weight residual 1.565 1.471 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O3 PO4 A1201 " pdb=" P PO4 A1201 " ideal model delta sigma weight residual 1.569 1.478 0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 94.10 - 102.09: 29 102.09 - 110.07: 1410 110.07 - 118.06: 4681 118.06 - 126.05: 4433 126.05 - 134.04: 105 Bond angle restraints: 10658 Sorted by residual: angle pdb=" CAM Y01 A1205 " pdb=" CAY Y01 A1205 " pdb=" OAW Y01 A1205 " ideal model delta sigma weight residual 111.19 125.92 -14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAM Y01 A1211 " pdb=" CAY Y01 A1211 " pdb=" OAW Y01 A1211 " ideal model delta sigma weight residual 111.19 125.83 -14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" CAM Y01 A1204 " pdb=" CAY Y01 A1204 " pdb=" OAW Y01 A1204 " ideal model delta sigma weight residual 111.19 125.69 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" N THR A 341 " pdb=" CA THR A 341 " pdb=" C THR A 341 " ideal model delta sigma weight residual 113.28 118.72 -5.44 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 111.40 106.30 5.10 1.22e+00 6.72e-01 1.75e+01 ... (remaining 10653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4427 16.07 - 32.13: 335 32.13 - 48.20: 82 48.20 - 64.26: 21 64.26 - 80.33: 5 Dihedral angle restraints: 4870 sinusoidal: 1896 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PRO A1026 " pdb=" C PRO A1026 " pdb=" N LEU A1027 " pdb=" CA LEU A1027 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR A 866 " pdb=" C TYR A 866 " pdb=" N CYS A 867 " pdb=" CA CYS A 867 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASN A1042 " pdb=" CB ASN A1042 " pdb=" CG ASN A1042 " pdb=" OD1 ASN A1042 " ideal model delta sinusoidal sigma weight residual 120.00 -165.51 -74.49 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1053 0.075 - 0.151: 223 0.151 - 0.226: 14 0.226 - 0.301: 4 0.301 - 0.377: 6 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CBG Y01 A1211 " pdb=" CAQ Y01 A1211 " pdb=" CBD Y01 A1211 " pdb=" CBI Y01 A1211 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CBG Y01 A1204 " pdb=" CAQ Y01 A1204 " pdb=" CBD Y01 A1204 " pdb=" CBI Y01 A1204 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.20e+00 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 -2.69 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1297 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 750 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" CD GLN A 750 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLN A 750 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 750 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 720 " -0.098 9.50e-02 1.11e+02 4.82e-02 6.20e+00 pdb=" NE ARG A 720 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 720 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 720 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 720 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 202 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" CD GLN A 202 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN A 202 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 202 " -0.013 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 42 2.52 - 3.12: 5657 3.12 - 3.71: 11696 3.71 - 4.31: 16556 4.31 - 4.90: 28750 Nonbonded interactions: 62701 Sorted by model distance: nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 1.930 2.170 nonbonded pdb=" O2 PO4 A1201 " pdb="MG MG A1202 " model vdw 1.950 2.170 nonbonded pdb=" OH TYR A 235 " pdb=" O PRO A 465 " model vdw 2.134 2.440 nonbonded pdb=" OE1 GLU A 766 " pdb=" NE2 HIS A 817 " model vdw 2.154 2.520 nonbonded pdb=" O THR A 510 " pdb="MG MG A1202 " model vdw 2.245 2.170 ... (remaining 62696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 6.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.010 0.124 7813 Z= 0.661 Angle : 0.960 14.735 10658 Z= 0.445 Chirality : 0.064 0.377 1300 Planarity : 0.005 0.053 1330 Dihedral : 13.024 80.326 2948 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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 (0.24), residues: 1016 helix: -0.59 (0.21), residues: 481 sheet: -0.38 (0.41), residues: 157 loop : -1.31 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 100 HIS 0.009 0.001 HIS A 385 PHE 0.015 0.002 PHE A1154 TYR 0.015 0.002 TYR A 235 ARG 0.039 0.002 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.918 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0693 time to fit residues: 59.0309 Evaluate side-chains 31 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.6980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7813 Z= 0.175 Angle : 0.522 6.194 10658 Z= 0.262 Chirality : 0.040 0.146 1300 Planarity : 0.005 0.062 1330 Dihedral : 9.107 76.992 1415 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.82 % Allowed : 8.05 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.51 (0.26), residues: 1016 helix: 1.08 (0.23), residues: 491 sheet: -0.02 (0.41), residues: 163 loop : -0.38 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.004 0.001 HIS A 775 PHE 0.012 0.001 PHE A1051 TYR 0.017 0.001 TYR A 931 ARG 0.005 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.855 Fit side-chains REVERT: A 102 LEU cc_start: 0.8692 (mm) cc_final: 0.8389 (tp) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.8494 time to fit residues: 40.4332 Evaluate side-chains 37 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.210 Angle : 0.504 6.705 10658 Z= 0.250 Chirality : 0.040 0.133 1300 Planarity : 0.004 0.064 1330 Dihedral : 8.616 71.379 1415 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.36 % Allowed : 9.96 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1016 helix: 1.77 (0.23), residues: 491 sheet: 0.16 (0.41), residues: 163 loop : -0.00 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.002 0.000 HIS A 775 PHE 0.010 0.001 PHE A 940 TYR 0.015 0.001 TYR A 931 ARG 0.003 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.791 Fit side-chains REVERT: A 102 LEU cc_start: 0.8702 (mm) cc_final: 0.8396 (tp) REVERT: A 1128 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7030 (mmp) outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.8599 time to fit residues: 43.7835 Evaluate side-chains 38 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7813 Z= 0.156 Angle : 0.494 12.266 10658 Z= 0.238 Chirality : 0.039 0.131 1300 Planarity : 0.004 0.061 1330 Dihedral : 8.175 68.829 1415 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.64 % Allowed : 11.46 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1016 helix: 2.14 (0.24), residues: 491 sheet: 0.41 (0.41), residues: 163 loop : 0.20 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.011 0.001 PHE A1051 TYR 0.015 0.001 TYR A 235 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.877 Fit side-chains REVERT: A 1128 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7002 (mmp) outliers start: 12 outliers final: 2 residues processed: 42 average time/residue: 0.8813 time to fit residues: 41.0601 Evaluate side-chains 35 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN A1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7813 Z= 0.311 Angle : 0.543 8.817 10658 Z= 0.264 Chirality : 0.042 0.133 1300 Planarity : 0.004 0.063 1330 Dihedral : 8.192 63.386 1415 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 12.01 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1016 helix: 2.11 (0.23), residues: 491 sheet: 0.49 (0.42), residues: 163 loop : 0.20 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.002 0.000 HIS A 831 PHE 0.011 0.001 PHE A 832 TYR 0.015 0.001 TYR A 235 ARG 0.002 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 33 time to evaluate : 0.779 Fit side-chains REVERT: A 1128 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7001 (mmp) outliers start: 17 outliers final: 9 residues processed: 47 average time/residue: 0.7652 time to fit residues: 40.0191 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7813 Z= 0.137 Angle : 0.487 9.680 10658 Z= 0.235 Chirality : 0.039 0.132 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.748 62.553 1415 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 12.28 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.05 (0.27), residues: 1016 helix: 2.36 (0.24), residues: 490 sheet: 0.67 (0.42), residues: 162 loop : 0.38 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.011 0.001 PHE A1051 TYR 0.013 0.001 TYR A 931 ARG 0.003 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.896 Fit side-chains REVERT: A 714 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 1128 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6977 (mmp) outliers start: 15 outliers final: 6 residues processed: 47 average time/residue: 0.8174 time to fit residues: 42.6242 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7813 Z= 0.244 Angle : 0.520 8.952 10658 Z= 0.250 Chirality : 0.041 0.133 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.737 59.979 1415 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 12.96 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.05 (0.27), residues: 1016 helix: 2.33 (0.24), residues: 492 sheet: 0.66 (0.42), residues: 162 loop : 0.43 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 831 PHE 0.010 0.001 PHE A 940 TYR 0.012 0.001 TYR A 931 ARG 0.001 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 33 time to evaluate : 0.852 Fit side-chains REVERT: A 714 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 1128 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6993 (mmp) outliers start: 15 outliers final: 7 residues processed: 47 average time/residue: 0.8756 time to fit residues: 45.7262 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 50.0000 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.8125 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7813 Z= 0.144 Angle : 0.529 10.551 10658 Z= 0.252 Chirality : 0.040 0.150 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.467 61.609 1415 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.64 % Allowed : 13.78 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.14 (0.27), residues: 1016 helix: 2.40 (0.24), residues: 492 sheet: 0.79 (0.44), residues: 150 loop : 0.43 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.009 0.001 PHE A1051 TYR 0.012 0.001 TYR A 931 ARG 0.001 0.000 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.883 Fit side-chains REVERT: A 714 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 1128 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6972 (mmp) outliers start: 12 outliers final: 5 residues processed: 44 average time/residue: 0.9261 time to fit residues: 44.8755 Evaluate side-chains 41 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7813 Z= 0.174 Angle : 0.542 13.749 10658 Z= 0.258 Chirality : 0.040 0.134 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.363 61.352 1415 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.19 (0.27), residues: 1016 helix: 2.43 (0.24), residues: 493 sheet: 0.82 (0.44), residues: 150 loop : 0.46 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 408 PHE 0.013 0.001 PHE A 531 TYR 0.012 0.001 TYR A 931 ARG 0.001 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.850 Fit side-chains REVERT: A 449 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7702 (tm) REVERT: A 714 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 1128 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6994 (mmp) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.9249 time to fit residues: 42.1337 Evaluate side-chains 40 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7813 Z= 0.192 Angle : 0.581 18.343 10658 Z= 0.273 Chirality : 0.040 0.156 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.257 60.926 1415 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 14.19 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.17 (0.27), residues: 1016 helix: 2.36 (0.23), residues: 499 sheet: 0.82 (0.44), residues: 150 loop : 0.51 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.009 0.001 PHE A 940 TYR 0.011 0.001 TYR A 931 ARG 0.001 0.000 ARG A 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.813 Fit side-chains REVERT: A 449 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7672 (tm) REVERT: A 714 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 1128 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6997 (mmp) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.8916 time to fit residues: 41.2844 Evaluate side-chains 41 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069202 restraints weight = 16712.868| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.21 r_work: 0.2903 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7813 Z= 0.174 Angle : 0.549 14.094 10658 Z= 0.262 Chirality : 0.040 0.166 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.135 60.958 1415 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 14.19 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.17 (0.27), residues: 1016 helix: 2.35 (0.24), residues: 499 sheet: 0.84 (0.44), residues: 150 loop : 0.51 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.009 0.001 PHE A 531 TYR 0.011 0.001 TYR A 931 ARG 0.001 0.000 ARG A 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.23 seconds wall clock time: 38 minutes 37.37 seconds (2317.37 seconds total)