Starting phenix.real_space_refine on Fri Feb 16 13:36:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/02_2024/8b9g_15931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/02_2024/8b9g_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_15931/02_2024/8b9g_15931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/02_2024/8b9g_15931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/02_2024/8b9g_15931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9g_15931/02_2024/8b9g_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.75, per 1000 atoms: 1.00 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: 3.35 Conformation dependent library (CDL) restraints added in 2.9 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: 3.74 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: 2.56 Time building geometry restraints manager: 3.38 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: 4680 32.93 - 65.86: 186 65.86 - 98.79: 17 98.79 - 131.73: 1 131.73 - 164.66: 1 Dihedral angle restraints: 4885 sinusoidal: 2087 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 4882 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: 1.170 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: 3.810 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 31.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.200 ------------------------------------------------------------------------------- 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 : 17.073 164.658 3063 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 : 0.917 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 1.5627 time to fit residues: 79.7080 Evaluate side-chains 32 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1121 VAL 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7944 Z= 0.278 Angle : 0.621 9.721 10811 Z= 0.303 Chirality : 0.044 0.167 1249 Planarity : 0.004 0.050 1358 Dihedral : 10.466 162.971 1207 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 2.26 % Allowed : 16.92 % Favored : 80.81 % 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: 1.46 (0.28), residues: 947 helix: 1.89 (0.25), residues: 450 sheet: 0.38 (0.44), residues: 146 loop : 0.11 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.003 0.001 HIS A 162 PHE 0.017 0.001 PHE A 667 TYR 0.011 0.001 TYR A 467 ARG 0.006 0.000 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 45 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 27 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 44 average time/residue: 1.2136 time to fit residues: 57.6124 Evaluate side-chains 29 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1117 ASP 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: 0.9980 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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** ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7944 Z= 0.227 Angle : 0.563 8.465 10811 Z= 0.274 Chirality : 0.043 0.160 1249 Planarity : 0.004 0.050 1358 Dihedral : 10.133 160.367 1203 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 1.31 % Allowed : 17.16 % Favored : 81.53 % 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 (0.28), residues: 947 helix: 1.86 (0.25), residues: 447 sheet: 0.16 (0.44), residues: 150 loop : 0.33 (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 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 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 outliers start: 10 outliers final: 3 residues processed: 37 average time/residue: 1.4927 time to fit residues: 59.0336 Evaluate side-chains 30 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1092 VAL 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: 0.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.0270 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7944 Z= 0.183 Angle : 0.553 8.887 10811 Z= 0.265 Chirality : 0.042 0.161 1249 Planarity : 0.004 0.049 1358 Dihedral : 10.003 158.098 1203 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 17.28 % Favored : 81.64 % 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: 448 sheet: 0.11 (0.44), residues: 150 loop : 0.36 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.016 0.001 PHE A 667 TYR 0.007 0.001 TYR A 467 ARG 0.008 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 35 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 805 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6906 (ttm) outliers start: 8 outliers final: 4 residues processed: 34 average time/residue: 1.4739 time to fit residues: 53.8773 Evaluate side-chains 32 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 chunk 83 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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** A 746 HIS ** A 972 GLN ** 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: 0.2474 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 : 0.528 8.927 10811 Z= 0.256 Chirality : 0.041 0.160 1249 Planarity : 0.004 0.048 1358 Dihedral : 9.865 154.605 1203 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.41 % Rotamer: Outliers : 1.31 % Allowed : 17.64 % 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: 1.57 (0.29), residues: 947 helix: 1.91 (0.25), residues: 448 sheet: 0.22 (0.44), residues: 149 loop : 0.41 (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 746 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 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 40 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.903 Fit side-chains REVERT: A 271 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8115 (tt) outliers start: 10 outliers final: 2 residues processed: 39 average time/residue: 1.3304 time to fit residues: 55.7736 Evaluate side-chains 30 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.0170 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.0370 chunk 89 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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** A 972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2624 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 : 0.540 10.038 10811 Z= 0.260 Chirality : 0.041 0.222 1249 Planarity : 0.004 0.054 1358 Dihedral : 9.780 154.787 1203 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 1.31 % Allowed : 17.64 % 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: 1.63 (0.29), residues: 947 helix: 1.96 (0.25), residues: 448 sheet: 0.26 (0.44), residues: 149 loop : 0.44 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.008 0.001 HIS A 941 PHE 0.015 0.001 PHE A 667 TYR 0.006 0.001 TYR A 467 ARG 0.013 0.000 ARG A 938 *********************** 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 39 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.973 Fit side-chains REVERT: A 271 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8122 (tt) outliers start: 10 outliers final: 2 residues processed: 38 average time/residue: 1.4869 time to fit residues: 60.3380 Evaluate side-chains 31 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7944 Z= 0.201 Angle : 0.570 13.511 10811 Z= 0.270 Chirality : 0.042 0.153 1249 Planarity : 0.004 0.046 1358 Dihedral : 9.804 157.849 1203 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 0.83 % Allowed : 18.24 % Favored : 80.93 % 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 (0.29), residues: 947 helix: 1.93 (0.25), residues: 448 sheet: 0.20 (0.44), residues: 150 loop : 0.44 (0.37), residues: 349 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 0.015 0.001 PHE A 667 TYR 0.008 0.001 TYR A 467 ARG 0.014 0.000 ARG A 938 *********************** 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 33 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.917 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 1.3317 time to fit residues: 47.4651 Evaluate side-chains 29 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7944 Z= 0.182 Angle : 0.568 13.681 10811 Z= 0.266 Chirality : 0.042 0.180 1249 Planarity : 0.004 0.046 1358 Dihedral : 9.772 157.541 1203 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 0.83 % Allowed : 18.12 % 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: 1.61 (0.29), residues: 947 helix: 1.93 (0.25), residues: 448 sheet: 0.23 (0.44), residues: 148 loop : 0.45 (0.37), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.012 0.000 ARG A 938 *********************** 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 33 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 1.2137 time to fit residues: 43.4432 Evaluate side-chains 30 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7938 moved from start: 0.2882 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= 0.147 Angle : 0.562 13.052 10811 Z= 0.262 Chirality : 0.041 0.198 1249 Planarity : 0.004 0.045 1358 Dihedral : 9.685 155.319 1203 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 0.48 % Allowed : 18.36 % 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: 1.69 (0.29), residues: 947 helix: 1.97 (0.25), residues: 448 sheet: 0.34 (0.45), residues: 147 loop : 0.49 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.010 0.000 ARG A 938 *********************** 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 30 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.955 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 1.3283 time to fit residues: 43.2046 Evaluate side-chains 29 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL 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: 0.8980 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 88 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.2961 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= 0.141 Angle : 0.567 13.069 10811 Z= 0.262 Chirality : 0.041 0.225 1249 Planarity : 0.004 0.045 1358 Dihedral : 9.639 154.644 1203 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 0.36 % Allowed : 18.59 % 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: 1.74 (0.29), residues: 947 helix: 2.02 (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 0.014 0.001 PHE A 667 TYR 0.006 0.001 TYR A 467 ARG 0.010 0.000 ARG A 938 ********************** 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 30 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.863 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 1.3794 time to fit residues: 44.6773 Evaluate side-chains 29 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.063690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049418 restraints weight = 47920.789| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.52 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3049 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= 0.144 Angle : 0.571 14.138 10811 Z= 0.262 Chirality : 0.041 0.219 1249 Planarity : 0.004 0.044 1358 Dihedral : 9.609 153.915 1203 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 0.36 % Allowed : 18.59 % 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: 1.78 (0.29), residues: 947 helix: 2.05 (0.25), residues: 448 sheet: 0.40 (0.45), residues: 147 loop : 0.51 (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 0.006 0.001 TYR A 467 ARG 0.010 0.000 ARG A 938 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.86 seconds wall clock time: 39 minutes 29.50 seconds (2369.50 seconds total)