Starting phenix.real_space_refine on Sun Dec 10 20:12:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/12_2023/8b9g_15931_updated.pdb" } resolution = 2.86 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= 0.005 sd= 0.019 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 7745 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 12 5.49 5 S 48 5.16 5 C 4890 2.51 5 N 1333 2.21 5 O 1494 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 ASP 148": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A TYR 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 847": "OD1" <-> "OD2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1101": "OE1" <-> "OE2" Residue "A ASP 1128": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 953, 7534 Classifications: {'peptide': 953} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 953, 7534 Classifications: {'peptide': 953} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7666 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 6} Time building chain proxies: 8.22, per 1000 atoms: 1.06 Number of scatterers: 7782 At special positions: 0 Unit cell: (91.242, 92.886, 103.572, 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 48 16.00 P 12 15.00 Al 1 13.00 F 4 9.00 O 1494 8.00 N 1333 7.00 C 4890 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=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 3.1 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: 1822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 7 sheets defined 44.5% alpha, 12.8% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 167 through 181 removed outlier: 4.207A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.736A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.669A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.583A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.895A 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 496 removed outlier: 4.183A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 544 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 621 through 629 Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.780A pdb=" N VAL A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' 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 843 Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.695A pdb=" N LEU A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 936 Processing helix chain 'A' and resid 940 through 950 Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 978 through 981 Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.725A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1076 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1102 through 1124 removed outlier: 3.642A pdb=" N LEU A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Proline residue: A1113 - end of helix 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 1147 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 555 through 559 removed outlier: 6.682A pdb=" N VAL A 535 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 405 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 537 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY A 407 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 481 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL A 438 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 483 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN A 440 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS A 485 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.974A pdb=" N GLY A 775 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE A 569 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS A 777 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 655 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL A 732 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 657 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP A 734 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 659 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 737 through 744 Processing sheet with id= E, first strand: chain 'A' and resid 1066 through 1068 removed outlier: 6.948A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1054 through 1057 removed outlier: 3.686A pdb=" N GLU A1054 " --> pdb=" O LYS A1064 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1082 through 1084 329 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2546 1.34 - 1.48: 1851 1.48 - 1.61: 3470 1.61 - 1.74: 0 1.74 - 1.88: 77 Bond restraints: 7944 Sorted by residual: bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.877 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.865 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.808 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" N GLU A 585 " pdb=" CA GLU A 585 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.40e-02 5.10e+03 3.98e+00 ... (remaining 7939 not shown) Histogram of bond angle deviations from ideal: 88.71 - 106.72: 270 106.72 - 124.73: 10397 124.73 - 142.73: 142 142.73 - 160.74: 0 160.74 - 178.75: 2 Bond angle restraints: 10811 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.69 -70.01 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.75 -69.12 3.00e+00 1.11e-01 5.31e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 89.09 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 88.71 20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 90.05 19.64 3.00e+00 1.11e-01 4.29e+01 ... (remaining 10806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 4659 32.93 - 65.86: 167 65.86 - 98.79: 17 98.79 - 131.73: 1 131.73 - 164.66: 1 Dihedral angle restraints: 4845 sinusoidal: 2047 harmonic: 2798 Sorted by residual: dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 4.66 -164.66 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -164.32 104.33 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA THR A 722 " pdb=" C THR A 722 " pdb=" N SER A 723 " pdb=" CA SER A 723 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 4842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 805 0.035 - 0.071: 299 0.071 - 0.106: 98 0.106 - 0.141: 45 0.141 - 0.176: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA GLU A1134 " pdb=" N GLU A1134 " pdb=" C GLU A1134 " pdb=" CB GLU A1134 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB ILE A 719 " pdb=" CA ILE A 719 " pdb=" CG1 ILE A 719 " pdb=" CG2 ILE A 719 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR A 414 " pdb=" CA THR A 414 " pdb=" OG1 THR A 414 " pdb=" CG2 THR A 414 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1246 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 261 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 262 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 865 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 866 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 866 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 866 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 146 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLN A 146 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 146 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 147 " 0.011 2.00e-02 2.50e+03 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 3350 2.94 - 3.59: 11731 3.59 - 4.25: 19626 4.25 - 4.90: 31711 Nonbonded interactions: 66430 Sorted by model distance: nonbonded pdb=" OG1 THR A 414 " pdb=" F4 ALF A1202 " model vdw 1.632 2.390 nonbonded pdb=" OD2 ASP A 507 " pdb=" F4 ALF A1202 " model vdw 1.858 2.390 nonbonded pdb=" O2A ADP A1201 " pdb=" O HOH A1301 " model vdw 2.056 2.440 nonbonded pdb=" O ILE A 574 " pdb=" OG1 THR A 578 " model vdw 2.139 2.440 nonbonded pdb=" OG1 THR A 414 " pdb="AL ALF A1202 " model vdw 2.167 2.760 ... (remaining 66425 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 33.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.005 0.192 7944 Z= 0.381 Angle : 1.198 70.010 10811 Z= 0.470 Chirality : 0.045 0.176 1249 Planarity : 0.005 0.049 1358 Dihedral : 16.623 164.658 3023 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.43 % Favored : 97.35 % Rotamer: Outliers : 1.43 % Allowed : 17.52 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.76 (0.24), residues: 449 sheet: 0.08 (0.41), residues: 165 loop : 0.17 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 932 HIS 0.004 0.001 HIS A 162 PHE 0.018 0.002 PHE A 667 TYR 0.018 0.002 TYR A 890 ARG 0.004 0.001 ARG A 739 *********************** 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 48 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.933 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 1.5411 time to fit residues: 78.4808 Evaluate side-chains 32 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 175 ASN A 196 HIS A 339 HIS A 435 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1011 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7944 Z= 0.277 Angle : 0.613 9.260 10811 Z= 0.300 Chirality : 0.044 0.166 1249 Planarity : 0.004 0.050 1358 Dihedral : 8.373 161.889 1163 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 2.98 % Allowed : 16.57 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.45 (0.28), residues: 947 helix: 1.89 (0.25), residues: 450 sheet: 0.30 (0.44), residues: 148 loop : 0.15 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 338 HIS 0.006 0.001 HIS A 646 PHE 0.017 0.001 PHE A 667 TYR 0.010 0.001 TYR A 467 ARG 0.006 0.001 ARG A 934 *********************** 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 51 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 27 time to evaluate : 0.884 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 50 average time/residue: 1.0989 time to fit residues: 59.7383 Evaluate side-chains 32 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7944 Z= 0.151 Angle : 0.538 7.815 10811 Z= 0.264 Chirality : 0.041 0.163 1249 Planarity : 0.004 0.049 1358 Dihedral : 7.883 156.125 1163 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.67 % Allowed : 16.45 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.59 (0.28), residues: 947 helix: 1.90 (0.25), residues: 450 sheet: 0.42 (0.47), residues: 138 loop : 0.34 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.015 0.001 PHE A 667 TYR 0.007 0.001 TYR A 467 ARG 0.006 0.000 ARG A 934 *********************** 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 42 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 1.253 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 40 average time/residue: 1.4500 time to fit residues: 62.4810 Evaluate side-chains 34 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.2390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 342 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7944 Z= 0.255 Angle : 0.579 8.983 10811 Z= 0.279 Chirality : 0.043 0.158 1249 Planarity : 0.004 0.049 1358 Dihedral : 7.920 159.258 1163 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 1.79 % Allowed : 16.81 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.47 (0.29), residues: 947 helix: 1.85 (0.25), residues: 449 sheet: 0.12 (0.44), residues: 150 loop : 0.35 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 691 PHE 0.017 0.001 PHE A 667 TYR 0.010 0.001 TYR A 467 ARG 0.007 0.000 ARG A 375 *********************** 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 42 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 28 time to evaluate : 1.010 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 39 average time/residue: 1.3545 time to fit residues: 56.6451 Evaluate side-chains 34 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7944 Z= 0.145 Angle : 0.525 8.269 10811 Z= 0.255 Chirality : 0.041 0.161 1249 Planarity : 0.004 0.048 1358 Dihedral : 7.674 153.951 1163 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 16.92 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 947 helix: 1.91 (0.25), residues: 449 sheet: 0.21 (0.44), residues: 149 loop : 0.41 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.006 0.001 TYR A 467 ARG 0.007 0.000 ARG A 375 *********************** 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 43 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 1.3720 time to fit residues: 61.9568 Evaluate side-chains 37 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.2006 time to fit residues: 2.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7944 Z= 0.221 Angle : 0.565 10.149 10811 Z= 0.269 Chirality : 0.042 0.154 1249 Planarity : 0.004 0.047 1358 Dihedral : 7.748 157.216 1163 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 1.67 % Allowed : 17.16 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.55 (0.29), residues: 947 helix: 1.93 (0.25), residues: 447 sheet: 0.11 (0.44), residues: 150 loop : 0.39 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 691 PHE 0.016 0.001 PHE A 667 TYR 0.009 0.001 TYR A 467 ARG 0.005 0.000 ARG A 375 *********************** 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 41 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 40 average time/residue: 1.3420 time to fit residues: 57.7715 Evaluate side-chains 36 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.1584 time to fit residues: 2.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7944 Z= 0.148 Angle : 0.527 9.372 10811 Z= 0.255 Chirality : 0.041 0.157 1249 Planarity : 0.004 0.047 1358 Dihedral : 7.577 153.361 1163 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.31 % Rotamer: Outliers : 1.31 % Allowed : 17.52 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.29), residues: 947 helix: 2.00 (0.25), residues: 448 sheet: 0.22 (0.44), residues: 149 loop : 0.42 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 941 PHE 0.015 0.001 PHE A 667 TYR 0.006 0.001 TYR A 467 ARG 0.006 0.000 ARG A 375 *********************** 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 38 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.976 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 37 average time/residue: 1.5009 time to fit residues: 59.9061 Evaluate side-chains 36 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.2966 time to fit residues: 2.8449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7944 Z= 0.143 Angle : 0.509 9.503 10811 Z= 0.245 Chirality : 0.041 0.175 1249 Planarity : 0.004 0.046 1358 Dihedral : 7.493 153.108 1163 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.31 % Allowed : 17.40 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 947 helix: 2.03 (0.25), residues: 448 sheet: 0.32 (0.45), residues: 147 loop : 0.49 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.015 0.001 PHE A 667 TYR 0.007 0.001 TYR A 467 ARG 0.005 0.000 ARG A 375 *********************** 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 37 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 1.0983 time to fit residues: 44.6011 Evaluate side-chains 35 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.036 7944 Z= 0.133 Angle : 0.505 10.183 10811 Z= 0.243 Chirality : 0.041 0.187 1249 Planarity : 0.003 0.046 1358 Dihedral : 7.417 152.056 1163 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.31 % Rotamer: Outliers : 1.31 % Allowed : 17.52 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.77 (0.29), residues: 947 helix: 2.06 (0.25), residues: 448 sheet: 0.38 (0.45), residues: 147 loop : 0.50 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.015 0.001 PHE A 667 TYR 0.006 0.001 TYR A 467 ARG 0.005 0.000 ARG A 375 *********************** 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 38 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 1.2483 time to fit residues: 48.9951 Evaluate side-chains 35 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.1331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7944 Z= 0.143 Angle : 0.516 10.368 10811 Z= 0.245 Chirality : 0.041 0.194 1249 Planarity : 0.003 0.045 1358 Dihedral : 7.389 152.259 1163 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.07 % Allowed : 17.76 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.82 (0.29), residues: 947 helix: 2.10 (0.25), residues: 448 sheet: 0.44 (0.45), residues: 147 loop : 0.52 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.015 0.001 PHE A 667 TYR 0.007 0.001 TYR A 467 ARG 0.005 0.000 ARG A 375 ********************** 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 35 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.947 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 1.1646 time to fit residues: 44.6063 Evaluate side-chains 35 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048623 restraints weight = 47387.976| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.67 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7944 Z= 0.149 Angle : 0.509 10.437 10811 Z= 0.243 Chirality : 0.041 0.189 1249 Planarity : 0.003 0.045 1358 Dihedral : 7.381 152.653 1163 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 1.31 % Allowed : 17.40 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.85 (0.29), residues: 947 helix: 2.12 (0.25), residues: 448 sheet: 0.45 (0.45), residues: 147 loop : 0.54 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.007 0.001 TYR A 467 ARG 0.005 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.94 seconds wall clock time: 39 minutes 53.43 seconds (2393.43 seconds total)