Starting phenix.real_space_refine on Mon Sep 23 16:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/09_2024/6osm_20186.cif" } resolution = 3.4 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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2570 2.51 5 N 710 2.21 5 O 820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4100 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.93, per 1000 atoms: 0.71 Number of scatterers: 4100 At special positions: 0 Unit cell: (100.7, 91.16, 40.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 820 8.00 N 710 7.00 C 2570 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 - 3.00 Amino acid : True - 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: 1.03 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.493A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL E 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL G 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 66 removed outlier: 6.246A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS C 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLN C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 66 removed outlier: 6.246A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS C 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLN C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.472A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 66 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.812A pdb=" N VAL F 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 710 1.28 - 1.35: 650 1.35 - 1.42: 170 1.42 - 1.49: 871 1.49 - 1.55: 1719 Bond restraints: 4120 Sorted by residual: bond pdb=" CB VAL C 55 " pdb=" CG2 VAL C 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB VAL I 55 " pdb=" CG2 VAL I 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB VAL J 55 " pdb=" CG2 VAL J 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CB VAL A 55 " pdb=" CG2 VAL A 55 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB VAL B 55 " pdb=" CG2 VAL B 55 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.56e+00 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 4941 1.84 - 3.69: 429 3.69 - 5.53: 160 5.53 - 7.38: 10 7.38 - 9.22: 40 Bond angle restraints: 5580 Sorted by residual: angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.54 113.32 9.22 1.82e+00 3.02e-01 2.57e+01 angle pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta sigma weight residual 122.54 113.35 9.19 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 122.54 113.35 9.19 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.54 113.36 9.18 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.54 113.36 9.18 1.82e+00 3.02e-01 2.54e+01 ... (remaining 5575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.65: 1757 8.65 - 17.30: 337 17.30 - 25.96: 196 25.96 - 34.61: 70 34.61 - 43.26: 30 Dihedral angle restraints: 2390 sinusoidal: 770 harmonic: 1620 Sorted by residual: dihedral pdb=" CA GLY H 67 " pdb=" C GLY H 67 " pdb=" N GLY H 68 " pdb=" CA GLY H 68 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY E 67 " pdb=" C GLY E 67 " pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY F 67 " pdb=" C GLY F 67 " pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 2387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 527 0.077 - 0.153: 151 0.153 - 0.230: 52 0.230 - 0.306: 0 0.306 - 0.382: 10 Chirality restraints: 740 Sorted by residual: chirality pdb=" CB ILE E 88 " pdb=" CA ILE E 88 " pdb=" CG1 ILE E 88 " pdb=" CG2 ILE E 88 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE B 88 " pdb=" CA ILE B 88 " pdb=" CG1 ILE B 88 " pdb=" CG2 ILE B 88 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 737 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 88 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ILE B 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 89 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 88 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ILE H 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE H 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA H 89 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 88 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ILE C 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE C 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 427 2.73 - 3.27: 3939 3.27 - 3.81: 6170 3.81 - 4.36: 6849 4.36 - 4.90: 14115 Nonbonded interactions: 31500 Sorted by model distance: nonbonded pdb=" O THR H 72 " pdb=" OG1 THR H 72 " model vdw 2.183 3.040 nonbonded pdb=" O THR B 72 " pdb=" OG1 THR B 72 " model vdw 2.183 3.040 nonbonded pdb=" O THR I 72 " pdb=" OG1 THR I 72 " model vdw 2.183 3.040 nonbonded pdb=" O THR J 72 " pdb=" OG1 THR J 72 " model vdw 2.183 3.040 nonbonded pdb=" O THR E 72 " pdb=" OG1 THR E 72 " model vdw 2.183 3.040 ... (remaining 31495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.012 0.063 4120 Z= 0.784 Angle : 1.453 9.221 5580 Z= 0.826 Chirality : 0.087 0.382 740 Planarity : 0.005 0.017 690 Dihedral : 14.061 43.261 1370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.48 % Favored : 65.52 % Rotamer: Outliers : 14.88 % Allowed : 11.95 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.34 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS B 50 PHE 0.005 0.002 PHE A 94 TYR 0.011 0.004 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 79 time to evaluate : 0.482 Fit side-chains REVERT: A 62 GLN cc_start: 0.8220 (pt0) cc_final: 0.7984 (pt0) REVERT: A 80 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7287 (mmtm) REVERT: B 57 GLU cc_start: 0.7667 (tt0) cc_final: 0.7362 (tp30) REVERT: B 62 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0) REVERT: B 80 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7598 (mptt) REVERT: C 57 GLU cc_start: 0.7183 (tt0) cc_final: 0.6793 (tt0) REVERT: C 62 GLN cc_start: 0.8185 (pt0) cc_final: 0.7836 (pt0) REVERT: E 92 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6268 (p) REVERT: F 92 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6446 (p) REVERT: G 92 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.6063 (p) REVERT: H 92 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6059 (p) REVERT: H 96 LYS cc_start: 0.6588 (tppp) cc_final: 0.6123 (mmmt) REVERT: I 92 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.5840 (p) REVERT: J 92 THR cc_start: 0.6243 (OUTLIER) cc_final: 0.5783 (p) outliers start: 61 outliers final: 35 residues processed: 120 average time/residue: 0.1376 time to fit residues: 21.0222 Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 76 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4120 Z= 0.194 Angle : 0.929 7.783 5580 Z= 0.485 Chirality : 0.059 0.196 740 Planarity : 0.003 0.014 690 Dihedral : 8.420 25.829 649 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.97 % Favored : 81.03 % Rotamer: Outliers : 8.05 % Allowed : 16.83 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.91 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 PHE 0.008 0.002 PHE C 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8142 (pt0) cc_final: 0.7904 (pt0) REVERT: A 80 LYS cc_start: 0.8092 (tptt) cc_final: 0.7387 (pttm) REVERT: B 57 GLU cc_start: 0.7576 (tt0) cc_final: 0.7233 (tp30) REVERT: B 62 GLN cc_start: 0.7905 (pt0) cc_final: 0.7498 (pt0) REVERT: B 80 LYS cc_start: 0.8268 (tptt) cc_final: 0.7151 (mptt) REVERT: C 57 GLU cc_start: 0.7315 (tt0) cc_final: 0.7041 (tt0) REVERT: D 52 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7452 (t) REVERT: D 80 LYS cc_start: 0.7997 (tptt) cc_final: 0.7222 (tptt) REVERT: E 52 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7397 (t) REVERT: F 52 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7584 (t) REVERT: G 52 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7593 (t) REVERT: H 38 LEU cc_start: 0.6379 (tt) cc_final: 0.5956 (mp) REVERT: H 52 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7354 (t) REVERT: H 96 LYS cc_start: 0.6617 (tppp) cc_final: 0.6019 (mmmt) outliers start: 33 outliers final: 23 residues processed: 121 average time/residue: 0.1219 time to fit residues: 19.2938 Evaluate side-chains 108 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4120 Z= 0.334 Angle : 1.043 7.633 5580 Z= 0.551 Chirality : 0.062 0.169 740 Planarity : 0.003 0.012 690 Dihedral : 9.619 41.367 619 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.38 % Favored : 73.62 % Rotamer: Outliers : 10.98 % Allowed : 15.85 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.02 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS F 50 PHE 0.012 0.002 PHE C 94 TYR 0.004 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 70 time to evaluate : 0.405 Fit side-chains REVERT: A 62 GLN cc_start: 0.8154 (pt0) cc_final: 0.7854 (pt0) REVERT: A 80 LYS cc_start: 0.8065 (tptt) cc_final: 0.7390 (pttm) REVERT: B 62 GLN cc_start: 0.8062 (pt0) cc_final: 0.7591 (pt0) REVERT: B 80 LYS cc_start: 0.8391 (tptt) cc_final: 0.7127 (mmtt) REVERT: C 57 GLU cc_start: 0.7363 (tt0) cc_final: 0.7141 (tt0) REVERT: H 38 LEU cc_start: 0.6328 (tt) cc_final: 0.5945 (mp) outliers start: 45 outliers final: 39 residues processed: 108 average time/residue: 0.1177 time to fit residues: 16.7813 Evaluate side-chains 107 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 68 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4120 Z= 0.405 Angle : 1.118 8.436 5580 Z= 0.593 Chirality : 0.064 0.187 740 Planarity : 0.004 0.015 690 Dihedral : 10.254 50.243 618 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.31 % Favored : 75.69 % Rotamer: Outliers : 10.98 % Allowed : 18.54 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.10 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS G 50 PHE 0.013 0.003 PHE D 94 TYR 0.004 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 72 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8178 (pt0) cc_final: 0.7846 (pt0) REVERT: A 80 LYS cc_start: 0.8079 (tptt) cc_final: 0.7448 (pttm) REVERT: B 62 GLN cc_start: 0.8135 (pt0) cc_final: 0.7716 (pt0) REVERT: B 80 LYS cc_start: 0.8360 (tptt) cc_final: 0.6915 (mmtt) REVERT: C 57 GLU cc_start: 0.7346 (tt0) cc_final: 0.7133 (tt0) outliers start: 45 outliers final: 40 residues processed: 110 average time/residue: 0.1120 time to fit residues: 16.5761 Evaluate side-chains 109 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 69 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4120 Z= 0.386 Angle : 1.083 8.013 5580 Z= 0.575 Chirality : 0.063 0.167 740 Planarity : 0.004 0.014 690 Dihedral : 10.072 47.018 618 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % Rotamer: Outliers : 11.71 % Allowed : 19.76 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.13 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.17), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS H 50 PHE 0.012 0.003 PHE D 94 TYR 0.004 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 71 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8256 (pt0) cc_final: 0.7982 (pt0) REVERT: A 80 LYS cc_start: 0.8049 (tptt) cc_final: 0.7376 (pttm) REVERT: B 80 LYS cc_start: 0.8220 (tptt) cc_final: 0.6743 (mmtt) REVERT: C 57 GLU cc_start: 0.7393 (tt0) cc_final: 0.7160 (tt0) outliers start: 48 outliers final: 44 residues processed: 111 average time/residue: 0.1091 time to fit residues: 16.3627 Evaluate side-chains 116 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 72 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4120 Z= 0.246 Angle : 0.939 7.348 5580 Z= 0.493 Chirality : 0.059 0.177 740 Planarity : 0.003 0.010 690 Dihedral : 8.968 37.839 618 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.03 % Favored : 78.97 % Rotamer: Outliers : 10.98 % Allowed : 21.71 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.04 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 PHE 0.008 0.002 PHE D 94 TYR 0.002 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 75 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8219 (pt0) cc_final: 0.7958 (pt0) REVERT: A 80 LYS cc_start: 0.7899 (tptt) cc_final: 0.7215 (pttm) REVERT: C 57 GLU cc_start: 0.7372 (tt0) cc_final: 0.7131 (tt0) REVERT: F 62 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7155 (tm-30) outliers start: 45 outliers final: 37 residues processed: 112 average time/residue: 0.1037 time to fit residues: 15.8553 Evaluate side-chains 109 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 71 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4120 Z= 0.456 Angle : 1.153 8.298 5580 Z= 0.617 Chirality : 0.067 0.178 740 Planarity : 0.004 0.015 690 Dihedral : 10.538 49.406 618 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.31 % Favored : 75.69 % Rotamer: Outliers : 11.22 % Allowed : 22.93 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.12 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.17), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.006 HIS G 50 PHE 0.014 0.003 PHE D 94 TYR 0.005 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 76 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8075 (tptt) cc_final: 0.7417 (pttm) REVERT: B 80 LYS cc_start: 0.8223 (tptt) cc_final: 0.6789 (mmtm) REVERT: C 57 GLU cc_start: 0.7274 (tt0) cc_final: 0.7068 (tt0) REVERT: D 61 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7990 (tp30) outliers start: 46 outliers final: 42 residues processed: 112 average time/residue: 0.1074 time to fit residues: 16.1588 Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 74 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.0270 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4120 Z= 0.333 Angle : 1.035 7.736 5580 Z= 0.550 Chirality : 0.063 0.174 740 Planarity : 0.003 0.013 690 Dihedral : 9.737 46.367 618 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.07 % Favored : 77.93 % Rotamer: Outliers : 10.98 % Allowed : 24.15 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.03 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS G 50 PHE 0.011 0.002 PHE D 94 TYR 0.003 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 75 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8346 (pt0) cc_final: 0.8083 (pt0) REVERT: A 80 LYS cc_start: 0.8020 (tptt) cc_final: 0.7311 (pttm) REVERT: C 57 GLU cc_start: 0.7386 (tt0) cc_final: 0.7153 (tt0) REVERT: D 61 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7290 (tt0) outliers start: 45 outliers final: 40 residues processed: 109 average time/residue: 0.1107 time to fit residues: 16.4550 Evaluate side-chains 116 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 75 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4120 Z= 0.361 Angle : 1.057 7.991 5580 Z= 0.563 Chirality : 0.064 0.171 740 Planarity : 0.003 0.014 690 Dihedral : 9.916 46.599 618 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.10 % Favored : 76.90 % Rotamer: Outliers : 11.22 % Allowed : 23.90 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.05 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS G 50 PHE 0.011 0.002 PHE D 94 TYR 0.004 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 0.462 Fit side-chains REVERT: A 62 GLN cc_start: 0.8371 (pt0) cc_final: 0.8097 (pt0) REVERT: A 80 LYS cc_start: 0.8145 (tptt) cc_final: 0.7358 (pttm) REVERT: C 57 GLU cc_start: 0.7383 (tt0) cc_final: 0.7149 (tt0) REVERT: D 61 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7328 (tt0) outliers start: 46 outliers final: 42 residues processed: 108 average time/residue: 0.1075 time to fit residues: 15.8401 Evaluate side-chains 116 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 73 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4120 Z= 0.321 Angle : 1.011 7.588 5580 Z= 0.536 Chirality : 0.062 0.166 740 Planarity : 0.003 0.012 690 Dihedral : 9.638 45.603 618 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.76 % Favored : 77.24 % Rotamer: Outliers : 10.98 % Allowed : 24.39 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.01 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS G 50 PHE 0.010 0.002 PHE D 94 TYR 0.003 0.001 TYR H 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 75 time to evaluate : 0.587 Fit side-chains REVERT: A 62 GLN cc_start: 0.8336 (pt0) cc_final: 0.8074 (pt0) REVERT: A 80 LYS cc_start: 0.8187 (tptt) cc_final: 0.7328 (pttm) REVERT: C 57 GLU cc_start: 0.7378 (tt0) cc_final: 0.7147 (tt0) REVERT: D 61 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 45 outliers final: 42 residues processed: 111 average time/residue: 0.1132 time to fit residues: 17.4345 Evaluate side-chains 118 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 75 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0050 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.218998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.186102 restraints weight = 4659.819| |-----------------------------------------------------------------------------| r_work (start): 0.4783 rms_B_bonded: 2.84 r_work: 0.4676 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4120 Z= 0.284 Angle : 0.961 7.454 5580 Z= 0.508 Chirality : 0.060 0.162 740 Planarity : 0.003 0.010 690 Dihedral : 9.261 42.520 618 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.28 % Favored : 76.72 % Rotamer: Outliers : 10.24 % Allowed : 25.12 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.94 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.008 0.001 PHE D 94 TYR 0.003 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.87 seconds wall clock time: 25 minutes 24.03 seconds (1524.03 seconds total)