Starting phenix.real_space_refine on Mon Sep 23 16:12:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqi_17111/09_2024/8oqi_17111.cif" } resolution = 3.1 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= 0.001 sd= 0.012 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 2370 2.51 5 N 660 2.21 5 O 780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3810 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 381 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.79, per 1000 atoms: 0.47 Number of scatterers: 3810 At special positions: 0 Unit cell: (90.1, 90.1, 41.34, 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 780 8.00 N 660 7.00 C 2370 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: 0.89 Conformation dependent library (CDL) restraints added in 659.1 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.834A pdb=" N VAL A 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS C 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL E 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL G 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS E 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL G 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL I 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS G 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.463A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU I 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA G 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.410A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN C 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN E 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.364A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.638A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR G 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS E 80 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR I 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS G 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.278A pdb=" N SER A 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER E 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.834A pdb=" N VAL B 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS B 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL D 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL F 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL H 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS F 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL J 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS H 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 57 removed outlier: 6.463A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU F 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR H 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU J 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA H 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.410A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.364A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL F 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL H 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.638A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.278A pdb=" N SER B 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER D 87 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER F 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 92 24 hydrogen bonds defined for protein. 72 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: 0.86 Time building geometry restraints manager: 1.02 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: 670 1.28 - 1.35: 610 1.35 - 1.41: 150 1.41 - 1.48: 205 1.48 - 1.54: 2195 Bond restraints: 3830 Sorted by residual: bond pdb=" N VAL E 63 " pdb=" CA VAL E 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.67e+00 bond pdb=" N VAL D 63 " pdb=" CA VAL D 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.65e+00 bond pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.52e+00 bond pdb=" N VAL A 63 " pdb=" CA VAL A 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.52e+00 bond pdb=" N VAL J 74 " pdb=" CA VAL J 74 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.50e+00 ... (remaining 3825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2450 1.12 - 2.25: 1223 2.25 - 3.37: 964 3.37 - 4.49: 431 4.49 - 5.62: 122 Bond angle restraints: 5190 Sorted by residual: angle pdb=" CA HIS H 50 " pdb=" CB HIS H 50 " pdb=" CG HIS H 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS C 50 " pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS A 50 " pdb=" CB HIS A 50 " pdb=" CG HIS A 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " pdb=" CG HIS E 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " pdb=" CG HIS I 50 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 5185 not shown) Histogram of dihedral angle deviations from ideal: 0.11 - 14.89: 1870 14.89 - 29.66: 220 29.66 - 44.43: 60 44.43 - 59.20: 30 59.20 - 73.97: 20 Dihedral angle restraints: 2200 sinusoidal: 700 harmonic: 1500 Sorted by residual: dihedral pdb=" CA GLU H 83 " pdb=" CB GLU H 83 " pdb=" CG GLU H 83 " pdb=" CD GLU H 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU I 83 " pdb=" CB GLU I 83 " pdb=" CG GLU I 83 " pdb=" CD GLU I 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.95 -55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.045: 100 0.045 - 0.087: 180 0.087 - 0.129: 220 0.129 - 0.171: 90 0.171 - 0.213: 90 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA LYS D 45 " pdb=" N LYS D 45 " pdb=" C LYS D 45 " pdb=" CB LYS D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LYS C 45 " pdb=" N LYS C 45 " pdb=" C LYS C 45 " pdb=" CB LYS C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 677 not shown) Planarity restraints: 650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 64 " -0.010 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR E 64 " 0.037 2.00e-02 2.50e+03 pdb=" O THR E 64 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN E 65 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 64 " 0.010 2.00e-02 2.50e+03 2.16e-02 4.64e+00 pdb=" C THR H 64 " -0.037 2.00e-02 2.50e+03 pdb=" O THR H 64 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN H 65 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 64 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR G 64 " 0.037 2.00e-02 2.50e+03 pdb=" O THR G 64 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN G 65 " -0.013 2.00e-02 2.50e+03 ... (remaining 647 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1772 2.95 - 3.44: 3537 3.44 - 3.93: 6175 3.93 - 4.41: 6924 4.41 - 4.90: 13698 Nonbonded interactions: 32106 Sorted by model distance: nonbonded pdb=" ND2 ASN G 65 " pdb=" O GLY G 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN B 65 " pdb=" O GLY B 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN J 65 " pdb=" O GLY J 68 " model vdw 2.465 3.120 ... (remaining 32101 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.013 0.039 3830 Z= 0.925 Angle : 2.008 5.618 5190 Z= 1.508 Chirality : 0.115 0.213 680 Planarity : 0.007 0.022 650 Dihedral : 18.286 73.975 1260 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 18.42 % Favored : 78.95 % 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: 0.22 (0.36), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.007 HIS D 50 PHE 0.002 0.001 PHE G 94 TYR 0.008 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.396 Fit side-chains REVERT: C 80 LYS cc_start: 0.9030 (tttp) cc_final: 0.8598 (tttm) REVERT: D 60 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7510 (mttp) REVERT: E 60 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7582 (mttp) REVERT: E 80 LYS cc_start: 0.9021 (tttp) cc_final: 0.8763 (tttp) REVERT: H 60 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7436 (mttt) outliers start: 10 outliers final: 2 residues processed: 88 average time/residue: 0.1854 time to fit residues: 19.5161 Evaluate side-chains 80 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3830 Z= 0.166 Angle : 0.435 2.557 5190 Z= 0.266 Chirality : 0.051 0.119 680 Planarity : 0.002 0.009 650 Dihedral : 5.591 40.925 562 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 17.89 % Favored : 79.47 % 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: -0.64 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.009 0.002 PHE F 94 TYR 0.001 0.000 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.410 Fit side-chains REVERT: F 43 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8231 (mttm) REVERT: J 43 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8106 (mttp) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.1930 time to fit residues: 16.5324 Evaluate side-chains 59 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 3830 Z= 0.571 Angle : 0.552 2.912 5190 Z= 0.339 Chirality : 0.056 0.140 680 Planarity : 0.003 0.014 650 Dihedral : 6.094 22.839 562 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.53 % Allowed : 22.63 % Favored : 76.84 % 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: -1.59 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS H 50 PHE 0.005 0.002 PHE B 94 TYR 0.006 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.388 Fit side-chains REVERT: F 43 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8371 (mttm) REVERT: G 43 LYS cc_start: 0.8590 (mttp) cc_final: 0.8215 (mttp) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.1703 time to fit residues: 13.2501 Evaluate side-chains 63 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3830 Z= 0.301 Angle : 0.441 2.230 5190 Z= 0.271 Chirality : 0.052 0.123 680 Planarity : 0.002 0.007 650 Dihedral : 5.207 15.543 560 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.63 % Allowed : 20.00 % Favored : 77.37 % 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: -1.55 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 PHE 0.003 0.001 PHE H 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.399 Fit side-chains REVERT: E 46 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7927 (mt-10) REVERT: I 79 GLN cc_start: 0.9193 (tt0) cc_final: 0.8972 (tt0) outliers start: 10 outliers final: 9 residues processed: 69 average time/residue: 0.1746 time to fit residues: 14.7333 Evaluate side-chains 67 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3830 Z= 0.378 Angle : 0.468 2.790 5190 Z= 0.286 Chirality : 0.053 0.121 680 Planarity : 0.002 0.008 650 Dihedral : 5.295 15.994 560 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.47 % Allowed : 19.21 % Favored : 76.32 % 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: -1.66 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.003 0.001 PHE H 94 TYR 0.004 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.410 Fit side-chains REVERT: I 79 GLN cc_start: 0.9208 (tt0) cc_final: 0.8990 (tt0) outliers start: 17 outliers final: 16 residues processed: 74 average time/residue: 0.1524 time to fit residues: 14.0668 Evaluate side-chains 73 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3830 Z= 0.280 Angle : 0.431 2.518 5190 Z= 0.264 Chirality : 0.052 0.123 680 Planarity : 0.002 0.007 650 Dihedral : 4.999 14.692 560 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.21 % Allowed : 19.74 % Favored : 76.05 % 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: -1.66 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.003 0.001 PHE H 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.363 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 73 average time/residue: 0.1473 time to fit residues: 13.4075 Evaluate side-chains 72 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8316 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3830 Z= 0.261 Angle : 0.423 2.246 5190 Z= 0.259 Chirality : 0.051 0.124 680 Planarity : 0.001 0.008 650 Dihedral : 4.872 13.718 560 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.74 % Allowed : 19.47 % Favored : 75.79 % 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: -1.66 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.018 0.002 PHE B 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.423 Fit side-chains outliers start: 18 outliers final: 17 residues processed: 73 average time/residue: 0.1578 time to fit residues: 14.3020 Evaluate side-chains 72 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3830 Z= 0.271 Angle : 0.422 2.205 5190 Z= 0.258 Chirality : 0.051 0.123 680 Planarity : 0.001 0.007 650 Dihedral : 4.852 13.732 560 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.47 % Allowed : 19.21 % Favored : 76.32 % 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: -1.66 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.003 0.001 PHE H 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.427 Fit side-chains REVERT: F 57 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8686 (mt-10) outliers start: 17 outliers final: 17 residues processed: 73 average time/residue: 0.1715 time to fit residues: 15.4606 Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8315 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3830 Z= 0.255 Angle : 0.415 2.117 5190 Z= 0.254 Chirality : 0.051 0.123 680 Planarity : 0.001 0.009 650 Dihedral : 4.790 13.318 560 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.74 % Allowed : 18.95 % Favored : 76.32 % 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: -1.65 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.021 0.002 PHE B 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.406 Fit side-chains REVERT: F 57 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8684 (mt-10) outliers start: 18 outliers final: 18 residues processed: 73 average time/residue: 0.1627 time to fit residues: 14.6376 Evaluate side-chains 75 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0980 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 3830 Z= 0.481 Angle : 0.496 2.708 5190 Z= 0.302 Chirality : 0.054 0.127 680 Planarity : 0.002 0.010 650 Dihedral : 5.358 15.122 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.47 % Allowed : 19.21 % Favored : 76.32 % 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: -1.84 (0.33), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 50 PHE 0.017 0.002 PHE B 94 TYR 0.005 0.002 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.431 Fit side-chains REVERT: F 57 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8658 (mt-10) outliers start: 17 outliers final: 17 residues processed: 74 average time/residue: 0.1733 time to fit residues: 15.6770 Evaluate side-chains 77 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108973 restraints weight = 4884.842| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.11 r_work: 0.3457 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3830 Z= 0.184 Angle : 0.397 2.070 5190 Z= 0.242 Chirality : 0.051 0.123 680 Planarity : 0.001 0.009 650 Dihedral : 4.612 12.269 560 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.95 % Allowed : 19.74 % Favored : 76.32 % 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: -1.72 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.020 0.001 PHE B 94 TYR 0.002 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1182.71 seconds wall clock time: 21 minutes 47.30 seconds (1307.30 seconds total)