Starting phenix.real_space_refine on Sat Mar 16 21:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9k_15934/03_2024/8b9k_15934_updated.pdb" } resolution = 4.04 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7434 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 42 5.49 5 S 47 5.16 5 C 5161 2.51 5 N 1447 2.21 5 O 1688 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7511 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 951, 7500 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 951, 7500 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 7633 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 847 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 37} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.62, per 1000 atoms: 1.03 Number of scatterers: 8390 At special positions: 0 Unit cell: (73.98, 106.038, 139.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 42 15.00 Al 1 13.00 F 4 9.00 O 1688 8.00 N 1447 7.00 C 5161 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: 3.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 9 sheets defined 40.7% alpha, 9.4% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.831A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 396 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 4.316A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 487 through 495 removed outlier: 4.127A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.905A pdb=" N ASP A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 830 through 842 Processing helix chain 'A' and resid 854 through 861 removed outlier: 3.619A pdb=" N ARG A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 removed outlier: 4.405A pdb=" N MET A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 921 through 936 Processing helix chain 'A' and resid 940 through 949 removed outlier: 4.330A pdb=" N ARG A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 974 Processing helix chain 'A' and resid 995 through 1007 Processing helix chain 'A' and resid 1102 through 1124 removed outlier: 4.163A pdb=" N LEU A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Proline residue: A1113 - end of helix removed outlier: 3.754A pdb=" N GLU A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1134 through 1146 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= B, first strand: chain 'A' and resid 402 through 405 removed outlier: 6.567A pdb=" N VAL A 535 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A 405 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 537 " --> pdb=" O ILE A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.921A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 567 through 569 Processing sheet with id= E, first strand: chain 'A' and resid 685 through 689 removed outlier: 6.053A pdb=" N THR A 711 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU A 688 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 713 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 730 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A 657 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A 732 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE A 659 " --> pdb=" O VAL A 732 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 737 through 744 removed outlier: 4.192A pdb=" N ALA A 753 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1027 through 1029 removed outlier: 6.062A pdb=" N LEU A1022 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A1015 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1054 through 1056 Processing sheet with id= I, first strand: chain 'A' and resid 1082 through 1085 removed outlier: 3.619A pdb=" N ILE A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2569 1.34 - 1.46: 1381 1.46 - 1.57: 4529 1.57 - 1.69: 82 1.69 - 1.81: 75 Bond restraints: 8636 Sorted by residual: bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.48e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 8631 not shown) Histogram of bond angle deviations from ideal: 89.38 - 107.43: 520 107.43 - 125.48: 11134 125.48 - 143.53: 241 143.53 - 161.58: 0 161.58 - 179.63: 2 Bond angle restraints: 11897 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 179.63 -70.95 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.62 -69.99 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 89.38 20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.36 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 89.66 19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 11892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 4870 20.48 - 40.95: 315 40.95 - 61.43: 100 61.43 - 81.91: 33 81.91 - 102.38: 6 Dihedral angle restraints: 5324 sinusoidal: 2531 harmonic: 2793 Sorted by residual: dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -162.38 102.38 1 2.00e+01 2.50e-03 2.91e+01 dihedral pdb=" CA TYR A 263 " pdb=" C TYR A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA MET A 629 " pdb=" C MET A 629 " pdb=" N LEU A 630 " pdb=" CA LEU A 630 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 868 0.027 - 0.054: 328 0.054 - 0.081: 103 0.081 - 0.108: 74 0.108 - 0.135: 22 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA VAL A 559 " pdb=" N VAL A 559 " pdb=" C VAL A 559 " pdb=" CB VAL A 559 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA PRO A 385 " pdb=" N PRO A 385 " pdb=" C PRO A 385 " pdb=" CB PRO A 385 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A 542 " pdb=" N ILE A 542 " pdb=" C ILE A 542 " pdb=" CB ILE A 542 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1392 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 440 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 441 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 390 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ARG A 390 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 390 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A1009 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A1010 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1010 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1010 " 0.020 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 381 2.71 - 3.26: 9148 3.26 - 3.80: 14799 3.80 - 4.35: 17812 4.35 - 4.90: 27588 Nonbonded interactions: 69728 Sorted by model distance: nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.160 2.440 nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.163 2.440 nonbonded pdb=" OD2 ASP A 993 " pdb=" OG SER A1150 " model vdw 2.195 2.440 nonbonded pdb=" O3B ADP A1201 " pdb=" F1 ALF A1202 " model vdw 2.201 2.390 nonbonded pdb=" OE1 GLU A 459 " pdb=" OG1 THR A 464 " model vdw 2.209 2.440 ... (remaining 69723 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 7.020 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 34.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 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 : 0.004 0.100 8636 Z= 0.219 Angle : 1.152 70.945 11897 Z= 0.460 Chirality : 0.039 0.135 1395 Planarity : 0.004 0.058 1381 Dihedral : 15.724 102.381 3506 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.48 % Favored : 88.89 % Rotamer: Outliers : 5.04 % Allowed : 10.79 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.89 (0.29), residues: 947 helix: 0.99 (0.26), residues: 413 sheet: -1.34 (0.42), residues: 157 loop : -2.06 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.000 HIS A 691 PHE 0.007 0.001 PHE A 475 TYR 0.008 0.001 TYR A 467 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7344 (mmp80) REVERT: A 602 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: A 643 LEU cc_start: 0.8885 (tp) cc_final: 0.8664 (tt) outliers start: 40 outliers final: 9 residues processed: 141 average time/residue: 0.1849 time to fit residues: 36.5930 Evaluate side-chains 79 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 922 HIS ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8636 Z= 0.214 Angle : 0.944 32.459 11897 Z= 0.401 Chirality : 0.044 0.429 1395 Planarity : 0.004 0.046 1381 Dihedral : 15.351 90.133 1654 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.52 % Favored : 90.05 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.02 (0.28), residues: 947 helix: 0.70 (0.26), residues: 408 sheet: -1.21 (0.44), residues: 150 loop : -1.96 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 328 HIS 0.008 0.001 HIS A 534 PHE 0.015 0.002 PHE A1045 TYR 0.009 0.001 TYR A 437 ARG 0.004 0.000 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 ILE cc_start: 0.8474 (mt) cc_final: 0.8256 (tp) REVERT: A 643 LEU cc_start: 0.8932 (tp) cc_final: 0.8692 (tt) REVERT: A 807 LEU cc_start: 0.8688 (mt) cc_final: 0.8483 (tt) REVERT: A 1003 LEU cc_start: 0.8245 (mt) cc_final: 0.7958 (mt) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1873 time to fit residues: 24.7829 Evaluate side-chains 73 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5676 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8636 Z= 0.325 Angle : 0.992 30.364 11897 Z= 0.433 Chirality : 0.045 0.333 1395 Planarity : 0.005 0.049 1381 Dihedral : 15.584 92.314 1654 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 32.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.53 % Favored : 88.04 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.38 (0.28), residues: 947 helix: 0.23 (0.25), residues: 407 sheet: -1.14 (0.44), residues: 139 loop : -2.03 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 328 HIS 0.007 0.002 HIS A 803 PHE 0.017 0.002 PHE A1077 TYR 0.011 0.002 TYR A 619 ARG 0.005 0.001 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2009 time to fit residues: 21.8353 Evaluate side-chains 55 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8636 Z= 0.169 Angle : 0.913 29.901 11897 Z= 0.384 Chirality : 0.043 0.264 1395 Planarity : 0.005 0.081 1381 Dihedral : 15.370 93.619 1654 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.10 % Favored : 90.48 % Rotamer: Outliers : 0.24 % Allowed : 1.68 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.18 (0.28), residues: 947 helix: 0.47 (0.26), residues: 406 sheet: -1.39 (0.42), residues: 145 loop : -1.85 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.003 0.001 HIS A 503 PHE 0.033 0.002 PHE A 778 TYR 0.012 0.001 TYR A 420 ARG 0.022 0.001 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.7824 (mm110) cc_final: 0.7588 (mm-40) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1799 time to fit residues: 22.0763 Evaluate side-chains 67 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8636 Z= 0.170 Angle : 0.899 29.857 11897 Z= 0.380 Chirality : 0.043 0.294 1395 Planarity : 0.004 0.040 1381 Dihedral : 15.161 92.408 1654 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.95 % Favored : 89.63 % Rotamer: Outliers : 0.24 % Allowed : 1.08 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.09 (0.28), residues: 947 helix: 0.58 (0.26), residues: 403 sheet: -1.31 (0.42), residues: 145 loop : -1.84 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 756 HIS 0.003 0.001 HIS A 803 PHE 0.011 0.001 PHE A1077 TYR 0.016 0.001 TYR A 437 ARG 0.007 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1750 time to fit residues: 21.3095 Evaluate side-chains 63 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.5640 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8636 Z= 0.254 Angle : 0.950 30.510 11897 Z= 0.410 Chirality : 0.043 0.287 1395 Planarity : 0.004 0.039 1381 Dihedral : 15.271 92.254 1654 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.16 % Favored : 89.42 % Rotamer: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.29 (0.28), residues: 947 helix: 0.37 (0.25), residues: 416 sheet: -1.34 (0.42), residues: 145 loop : -2.01 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 328 HIS 0.006 0.001 HIS A 803 PHE 0.018 0.002 PHE A1077 TYR 0.009 0.001 TYR A 890 ARG 0.004 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.7534 (ttt) cc_final: 0.7113 (ttt) REVERT: A 872 MET cc_start: 0.7532 (mmp) cc_final: 0.7137 (mmp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1998 time to fit residues: 22.1239 Evaluate side-chains 59 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8636 Z= 0.185 Angle : 0.902 30.248 11897 Z= 0.382 Chirality : 0.042 0.276 1395 Planarity : 0.005 0.083 1381 Dihedral : 15.236 93.367 1654 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.95 % Favored : 89.63 % Rotamer: Outliers : 0.36 % Allowed : 0.96 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.14 (0.28), residues: 947 helix: 0.51 (0.26), residues: 414 sheet: -1.47 (0.43), residues: 131 loop : -1.83 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 756 HIS 0.003 0.001 HIS A 803 PHE 0.014 0.001 PHE A1077 TYR 0.007 0.001 TYR A 890 ARG 0.009 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.1736 time to fit residues: 20.0814 Evaluate side-chains 62 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.5661 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8636 Z= 0.248 Angle : 0.943 30.952 11897 Z= 0.407 Chirality : 0.043 0.285 1395 Planarity : 0.005 0.071 1381 Dihedral : 15.355 96.793 1654 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.79 % Favored : 88.78 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.28), residues: 947 helix: 0.32 (0.25), residues: 414 sheet: -1.37 (0.43), residues: 142 loop : -1.93 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 756 HIS 0.006 0.001 HIS A 803 PHE 0.021 0.002 PHE A1077 TYR 0.010 0.001 TYR A 263 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1906 time to fit residues: 20.6205 Evaluate side-chains 58 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.5764 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8636 Z= 0.286 Angle : 0.970 31.533 11897 Z= 0.427 Chirality : 0.045 0.272 1395 Planarity : 0.005 0.069 1381 Dihedral : 15.726 103.055 1654 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.01 % Favored : 88.57 % Rotamer: Outliers : 0.24 % Allowed : 0.72 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.43 (0.28), residues: 947 helix: 0.14 (0.25), residues: 403 sheet: -1.55 (0.40), residues: 159 loop : -1.79 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1095 HIS 0.007 0.002 HIS A 803 PHE 0.022 0.002 PHE A1077 TYR 0.015 0.002 TYR A 263 ARG 0.008 0.001 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1933 time to fit residues: 20.0688 Evaluate side-chains 56 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 83 optimal weight: 0.0020 chunk 24 optimal weight: 5.9990 overall best weight: 1.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A 686 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8636 Z= 0.192 Angle : 0.935 30.301 11897 Z= 0.401 Chirality : 0.043 0.254 1395 Planarity : 0.005 0.059 1381 Dihedral : 15.542 100.145 1654 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.58 % Favored : 88.99 % Rotamer: Outliers : 0.24 % Allowed : 0.36 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.36 (0.28), residues: 947 helix: 0.23 (0.25), residues: 409 sheet: -1.56 (0.41), residues: 149 loop : -1.80 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 756 HIS 0.004 0.001 HIS A 984 PHE 0.014 0.002 PHE A1077 TYR 0.021 0.002 TYR A 890 ARG 0.010 0.000 ARG A 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 805 MET cc_start: 0.7339 (mmm) cc_final: 0.7064 (mmp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1951 time to fit residues: 21.0824 Evaluate side-chains 59 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.059145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.038357 restraints weight = 217044.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.040375 restraints weight = 102541.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.041702 restraints weight = 66950.605| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8636 Z= 0.185 Angle : 0.923 30.322 11897 Z= 0.393 Chirality : 0.043 0.254 1395 Planarity : 0.005 0.056 1381 Dihedral : 15.404 98.836 1654 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.69 % Favored : 88.89 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.28), residues: 947 helix: 0.32 (0.26), residues: 411 sheet: -1.62 (0.43), residues: 137 loop : -1.83 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 756 HIS 0.004 0.001 HIS A 984 PHE 0.015 0.002 PHE A1077 TYR 0.042 0.002 TYR A 890 ARG 0.008 0.000 ARG A 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.40 seconds wall clock time: 33 minutes 1.36 seconds (1981.36 seconds total)