Starting phenix.real_space_refine (version: dev) on Mon Apr 4 17:33:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/04_2022/7n78_24223_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/04_2022/7n78_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_24223/04_2022/7n78_24223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/04_2022/7n78_24223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/04_2022/7n78_24223_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n78_24223/04_2022/7n78_24223_trim_updated.pdb" } resolution = 3.0 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= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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, 'PO4': 1, 'PC1': 2, 'LMT': 3, 'Y01': 3, 'SPM': 1} Classifications: {'undetermined': 11, 'water': 3, 'peptide': 1030} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 68, 'TRANS': 958, None: 14, 'PCIS': 3} 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: 505 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: 5.31, per 1000 atoms: 0.69 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: 3.58 Conformation dependent library (CDL) restraints added in 1.2 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... running ksdssp... Secondary structure from input PDB file: 39 helices and 9 sheets defined 46.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.847A pdb=" N ARG A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.717A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 252 through 283 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 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 417 through 444 Processing helix chain 'A' and resid 449 through 463 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 468 through 486 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 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 497 through 500 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 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.634A pdb=" N ALA A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 4.392A pdb=" N ALA A 669 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 670 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 671 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 677 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 704 through 707 No H-bonds generated for 'chain 'A' and resid 704 through 707' Processing helix chain 'A' and resid 725 through 736 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 836 through 842 Processing helix chain 'A' and resid 851 through 864 removed outlier: 3.650A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.542A pdb=" N CYS A 878 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY A 879 " --> pdb=" O ASN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 947 Proline residue: A 912 - end of helix removed outlier: 3.534A pdb=" N LEU A 937 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 945 " --> pdb=" O SER A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 964 through 973 removed outlier: 3.756A pdb=" N THR A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1019 Processing helix chain 'A' and resid 1040 through 1060 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) 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 1091 Processing helix chain 'A' and resid 1109 through 1144 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 1153 through 1163 Processing sheet with id= A, first strand: chain 'A' and resid 88 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.791A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id= C, 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: 6.840A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.234A pdb=" N ASN A 336 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE A 375 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 488 through 490 Processing sheet with id= F, first strand: chain 'A' and resid 740 through 743 removed outlier: 6.485A pdb=" N VAL A 886 " --> pdb=" O MET A 870 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY A 872 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 888 " --> pdb=" O GLY A 872 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 557 through 559 Processing sheet with id= H, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.567A pdb=" N SER A 618 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 635 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG A 622 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 783 through 789 removed outlier: 3.612A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A 820 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 846 " --> pdb=" O LEU A 820 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 987 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: 2.87 Time building geometry restraints manager: 3.62 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 - 15.67: 4222 15.67 - 31.33: 337 31.33 - 47.00: 81 47.00 - 62.66: 20 62.66 - 78.33: 3 Dihedral angle restraints: 4663 sinusoidal: 1689 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 4660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1055 0.075 - 0.151: 223 0.151 - 0.226: 12 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: 5737 3.12 - 3.71: 11726 3.71 - 4.31: 16671 4.31 - 4.90: 28769 Nonbonded interactions: 62945 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 62940 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: 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. 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: 1.230 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: 7.150 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 26.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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= 0.647 Angle : 0.908 14.735 10658 Z= 0.433 Chirality : 0.063 0.377 1300 Planarity : 0.005 0.053 1330 Dihedral : 12.874 78.331 2741 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 % 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 *********************** 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 : 0.876 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0413 time to fit residues: 57.7179 Evaluate side-chains 31 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2201 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1081 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= 0.184 Angle : 0.519 6.502 10658 Z= 0.264 Chirality : 0.040 0.153 1300 Planarity : 0.005 0.059 1330 Dihedral : 8.084 59.359 1208 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.09 % 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: 0.31 (0.26), residues: 1016 helix: 0.87 (0.23), residues: 484 sheet: -0.13 (0.41), residues: 163 loop : -0.36 (0.32), residues: 369 *********************** 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 46 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 1.005 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 0.8856 time to fit residues: 42.3356 Evaluate side-chains 38 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.2457 ------------------------------------------------------------------------------- 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: 40.0000 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 7813 Z= 0.147 Angle : 0.478 6.971 10658 Z= 0.240 Chirality : 0.040 0.161 1300 Planarity : 0.005 0.062 1330 Dihedral : 7.357 58.440 1208 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.36 % 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: 0.90 (0.27), residues: 1016 helix: 1.32 (0.24), residues: 486 sheet: 0.18 (0.43), residues: 151 loop : -0.04 (0.32), residues: 379 *********************** 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 47 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.992 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 0.8861 time to fit residues: 43.2336 Evaluate side-chains 37 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.2911 ------------------------------------------------------------------------------- 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: 0.1980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 7813 Z= 0.154 Angle : 0.477 7.386 10658 Z= 0.235 Chirality : 0.039 0.128 1300 Planarity : 0.004 0.061 1330 Dihedral : 6.970 57.983 1208 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.64 % 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: 1.13 (0.27), residues: 1016 helix: 1.44 (0.24), residues: 490 sheet: 0.48 (0.43), residues: 151 loop : 0.08 (0.32), residues: 375 *********************** 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 51 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.908 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 47 average time/residue: 0.7534 time to fit residues: 39.7915 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.1926 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 7813 Z= 0.269 Angle : 0.529 11.424 10658 Z= 0.256 Chirality : 0.041 0.187 1300 Planarity : 0.005 0.084 1330 Dihedral : 6.969 55.895 1208 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.77 % 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: 1.20 (0.27), residues: 1016 helix: 1.48 (0.24), residues: 490 sheet: 0.55 (0.43), residues: 151 loop : 0.13 (0.32), residues: 375 *********************** 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 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.848 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 0.7406 time to fit residues: 39.7787 Evaluate side-chains 41 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 30.0000 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 40.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 7813 Z= 0.221 Angle : 0.523 9.085 10658 Z= 0.253 Chirality : 0.040 0.135 1300 Planarity : 0.005 0.060 1330 Dihedral : 6.857 57.057 1208 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.91 % 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: 1.30 (0.27), residues: 1016 helix: 1.56 (0.24), residues: 488 sheet: 0.51 (0.42), residues: 157 loop : 0.23 (0.33), residues: 371 *********************** 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 51 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 1.056 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 48 average time/residue: 0.8144 time to fit residues: 43.5311 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0621 time to fit residues: 1.2152 ------------------------------------------------------------------------------- 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: 7.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 40.0000 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7813 Z= 0.167 Angle : 0.517 9.082 10658 Z= 0.249 Chirality : 0.040 0.148 1300 Planarity : 0.004 0.060 1330 Dihedral : 6.634 58.517 1208 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.36 % 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: 1.46 (0.27), residues: 1016 helix: 1.65 (0.24), residues: 488 sheet: 0.76 (0.43), residues: 143 loop : 0.30 (0.32), residues: 385 *********************** 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 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.975 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.7989 time to fit residues: 43.2015 Evaluate side-chains 43 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0768 time to fit residues: 1.4296 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 9 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 7813 Z= 0.151 Angle : 0.516 9.236 10658 Z= 0.249 Chirality : 0.039 0.133 1300 Planarity : 0.004 0.059 1330 Dihedral : 6.450 55.979 1208 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.50 % 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: 1.53 (0.27), residues: 1016 helix: 1.64 (0.24), residues: 495 sheet: 0.76 (0.44), residues: 137 loop : 0.43 (0.32), residues: 384 *********************** 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 49 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.946 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.8448 time to fit residues: 44.3218 Evaluate side-chains 45 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0738 time to fit residues: 1.3878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 84 optimal weight: 0.0060 chunk 88 optimal weight: 0.0020 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 overall best weight: 0.2002 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7813 Z= 0.118 Angle : 0.548 15.320 10658 Z= 0.259 Chirality : 0.039 0.168 1300 Planarity : 0.004 0.060 1330 Dihedral : 6.259 56.289 1208 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 1.23 % 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: 1.64 (0.27), residues: 1016 helix: 1.75 (0.25), residues: 490 sheet: 0.70 (0.42), residues: 150 loop : 0.51 (0.33), residues: 376 *********************** 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 47 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.972 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.8405 time to fit residues: 43.2126 Evaluate side-chains 43 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3322 ------------------------------------------------------------------------------- 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: 40.0000 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7813 Z= 0.209 Angle : 0.572 13.771 10658 Z= 0.272 Chirality : 0.041 0.156 1300 Planarity : 0.004 0.060 1330 Dihedral : 6.344 59.080 1208 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.09 % 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: 1.64 (0.27), residues: 1016 helix: 1.72 (0.24), residues: 495 sheet: 0.83 (0.45), residues: 137 loop : 0.49 (0.32), residues: 384 ********************** 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 45 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.005 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.8564 time to fit residues: 42.1025 Evaluate side-chains 42 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.2732 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 4 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.100764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070431 restraints weight = 16769.813| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.22 r_work: 0.3093 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.3073 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work: 0.3063 rms_B_bonded: 3.04 restraints_weight: 0.0625 r_work: 0.3052 rms_B_bonded: 3.09 restraints_weight: 0.0312 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.0156 r_work: 0.3032 rms_B_bonded: 3.22 restraints_weight: 0.0078 r_work: 0.3021 rms_B_bonded: 3.31 restraints_weight: 0.0039 r_work: 0.3010 rms_B_bonded: 3.41 restraints_weight: 0.0020 r_work: 0.2999 rms_B_bonded: 3.52 restraints_weight: 0.0010 r_work: 0.2988 rms_B_bonded: 3.64 restraints_weight: 0.0005 r_work: 0.2977 rms_B_bonded: 3.77 restraints_weight: 0.0002 r_work: 0.2965 rms_B_bonded: 3.92 restraints_weight: 0.0001 r_work: 0.2953 rms_B_bonded: 4.08 restraints_weight: 0.0001 r_work: 0.2940 rms_B_bonded: 4.25 restraints_weight: 0.0000 r_work: 0.2927 rms_B_bonded: 4.44 restraints_weight: 0.0000 r_work: 0.2914 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work: 0.2901 rms_B_bonded: 4.86 restraints_weight: 0.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7813 Z= 0.150 Angle : 0.560 13.749 10658 Z= 0.264 Chirality : 0.040 0.162 1300 Planarity : 0.004 0.060 1330 Dihedral : 6.198 56.174 1208 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.95 % 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: 1.70 (0.27), residues: 1016 helix: 1.75 (0.24), residues: 494 sheet: 0.76 (0.42), residues: 150 loop : 0.58 (0.34), residues: 372 =============================================================================== Job complete usr+sys time: 1970.85 seconds wall clock time: 36 minutes 12.81 seconds (2172.81 seconds total)