Starting phenix.real_space_refine on Wed Jun 3 09:54:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.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/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijp_60637/06_2026/9ijp_60637.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians P 24 5.49 5 C 1644 2.51 5 N 456 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2730 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'7TT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: L, I, E, B Time building chain proxies: 0.74, per 1000 atoms: 0.27 Number of scatterers: 2730 At special positions: 0 Unit cell: (113.71, 93.79, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 24 15.00 O 606 8.00 N 456 7.00 C 1644 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: 0.16 Conformation dependent library (CDL) restraints added in 132.5 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 61.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 45 through 55 removed outlier: 6.327A pdb=" N LYS C 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N HIS G 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL C 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N VAL G 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR G 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL I 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS C 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY I 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 58 through 66 removed outlier: 6.776A pdb=" N THR G 59 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR C 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLN I 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR I 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL I 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 69 through 82 removed outlier: 6.593A pdb=" N ALA C 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR G 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL G 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY C 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N ALA G 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N THR C 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ALA G 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS G 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN C 79 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL G 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 81 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR I 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA C 76 " --> pdb=" O THR I 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 86 through 92 removed outlier: 6.848A pdb=" N SER C 87 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE G 88 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLY C 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ALA I 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE C 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA I 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA C 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 95 through 97 removed outlier: 6.748A pdb=" N LYS C 96 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 45 through 55 removed outlier: 6.327A pdb=" N LYS L 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL E 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY L 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N HIS E 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL L 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N VAL E 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY L 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA L 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL L 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 49 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS L 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 51 " --> pdb=" O HIS L 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 66 removed outlier: 6.775A pdb=" N THR E 59 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR L 59 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN B 62 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU L 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 64 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL L 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 66 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN L 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82 removed outlier: 6.593A pdb=" N ALA L 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR E 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL L 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL E 74 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY L 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ALA E 76 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N THR L 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ALA E 78 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL L 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS E 80 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN L 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL E 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR L 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL L 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA L 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92 removed outlier: 6.848A pdb=" N SER L 87 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 88 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLY L 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N ALA B 89 " --> pdb=" O GLY L 86 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE L 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 91 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA L 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 95 through 97 removed outlier: 6.748A pdb=" N LYS L 96 " --> pdb=" O LYS E 97 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 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: 0.23 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 462 1.31 - 1.39: 504 1.39 - 1.48: 440 1.48 - 1.56: 1294 1.56 - 1.65: 36 Bond restraints: 2736 Sorted by residual: bond pdb=" O13 7TT C 202 " pdb=" P11 7TT C 202 " ideal model delta sigma weight residual 1.595 1.648 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" O13 7TT L 203 " pdb=" P11 7TT L 203 " ideal model delta sigma weight residual 1.595 1.648 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" O13 7TT L 202 " pdb=" P11 7TT L 202 " ideal model delta sigma weight residual 1.595 1.647 -0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" O13 7TT C 203 " pdb=" P11 7TT C 203 " ideal model delta sigma weight residual 1.595 1.647 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" O13 7TT C 201 " pdb=" P11 7TT C 201 " ideal model delta sigma weight residual 1.595 1.647 -0.052 2.00e-02 2.50e+03 6.80e+00 ... (remaining 2731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 3564 2.76 - 5.53: 114 5.53 - 8.29: 8 8.29 - 11.05: 34 11.05 - 13.82: 12 Bond angle restraints: 3732 Sorted by residual: angle pdb=" P08 7TT C 203 " pdb=" O10 7TT C 203 " pdb=" P11 7TT C 203 " ideal model delta sigma weight residual 135.25 121.43 13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" P08 7TT L 201 " pdb=" O10 7TT L 201 " pdb=" P11 7TT L 201 " ideal model delta sigma weight residual 135.25 121.44 13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" P08 7TT L 203 " pdb=" O10 7TT L 203 " pdb=" P11 7TT L 203 " ideal model delta sigma weight residual 135.25 121.44 13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" P08 7TT C 201 " pdb=" O10 7TT C 201 " pdb=" P11 7TT C 201 " ideal model delta sigma weight residual 135.25 121.48 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" P08 7TT C 202 " pdb=" O10 7TT C 202 " pdb=" P11 7TT C 202 " ideal model delta sigma weight residual 135.25 121.48 13.77 3.00e+00 1.11e-01 2.11e+01 ... (remaining 3727 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 29.85: 1530 29.85 - 59.68: 94 59.68 - 89.52: 6 89.52 - 119.36: 8 119.36 - 149.20: 18 Dihedral angle restraints: 1656 sinusoidal: 630 harmonic: 1026 Sorted by residual: dihedral pdb=" O09 7TT C 202 " pdb=" O10 7TT C 202 " pdb=" P08 7TT C 202 " pdb=" P11 7TT C 202 " ideal model delta sinusoidal sigma weight residual 161.14 -49.66 -149.20 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" O09 7TT C 203 " pdb=" O10 7TT C 203 " pdb=" P08 7TT C 203 " pdb=" P11 7TT C 203 " ideal model delta sinusoidal sigma weight residual 161.14 -49.70 -149.16 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" O09 7TT L 202 " pdb=" O10 7TT L 202 " pdb=" P08 7TT L 202 " pdb=" P11 7TT L 202 " ideal model delta sinusoidal sigma weight residual 161.14 -49.72 -149.14 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 1653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 157 0.026 - 0.052: 176 0.052 - 0.078: 51 0.078 - 0.104: 38 0.104 - 0.130: 46 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL E 66 " pdb=" N VAL E 66 " pdb=" C VAL E 66 " pdb=" CB VAL E 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL G 66 " pdb=" N VAL G 66 " pdb=" C VAL G 66 " pdb=" CB VAL G 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL I 66 " pdb=" N VAL I 66 " pdb=" C VAL I 66 " pdb=" CB VAL I 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 41 " -0.005 2.00e-02 2.50e+03 9.24e-03 8.53e-01 pdb=" C GLY G 41 " 0.016 2.00e-02 2.50e+03 pdb=" O GLY G 41 " -0.006 2.00e-02 2.50e+03 pdb=" N SER G 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 41 " 0.005 2.00e-02 2.50e+03 9.15e-03 8.37e-01 pdb=" C GLY L 41 " -0.016 2.00e-02 2.50e+03 pdb=" O GLY L 41 " 0.006 2.00e-02 2.50e+03 pdb=" N SER L 42 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 41 " 0.005 2.00e-02 2.50e+03 9.09e-03 8.26e-01 pdb=" C GLY B 41 " -0.016 2.00e-02 2.50e+03 pdb=" O GLY B 41 " 0.006 2.00e-02 2.50e+03 pdb=" N SER B 42 " 0.005 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1105 2.92 - 3.41: 2412 3.41 - 3.91: 3911 3.91 - 4.40: 4332 4.40 - 4.90: 8954 Nonbonded interactions: 20714 Sorted by model distance: nonbonded pdb=" NZ LYS C 60 " pdb=" O09 7TT C 201 " model vdw 2.422 3.120 nonbonded pdb=" NZ LYS G 60 " pdb=" O24 7TT C 201 " model vdw 2.426 3.120 nonbonded pdb=" NZ LYS L 60 " pdb=" O09 7TT L 201 " model vdw 2.438 3.120 nonbonded pdb=" NZ LYS E 60 " pdb=" O24 7TT L 201 " model vdw 2.445 3.120 nonbonded pdb=" NZ LYS C 97 " pdb=" O12 7TT C 202 " model vdw 2.520 3.120 ... (remaining 20709 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'E' selection = chain 'B' } 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: 2.860 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.053 2736 Z= 0.426 Angle : 1.537 13.816 3732 Z= 0.609 Chirality : 0.055 0.130 468 Planarity : 0.002 0.009 444 Dihedral : 26.271 149.196 1008 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR G 39 PHE 0.013 0.004 PHE C 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.43 ( 2736) covalent geometry : angle 1.53741 / 0.61 ( 3732) hydrogen bonds : bond 0.15277 / 9.20 ( 56) hydrogen bonds : angle 7.92475 / 5.33 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.103 Fit side-chains REVERT: G 45 LYS cc_start: 0.8972 (mttt) cc_final: 0.8719 (mttp) REVERT: B 83 GLU cc_start: 0.7916 (tt0) cc_final: 0.7701 (tt0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1074 time to fit residues: 5.8240 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN I 62 GLN L 62 GLN E 62 GLN B 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.166147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126250 restraints weight = 2832.828| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.08 r_work: 0.3640 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2736 Z= 0.144 Angle : 0.544 4.938 3732 Z= 0.281 Chirality : 0.053 0.156 468 Planarity : 0.002 0.006 444 Dihedral : 33.738 173.835 486 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.93 % Allowed : 14.07 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR L 39 PHE 0.012 0.003 PHE I 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 2736) covalent geometry : angle 0.54421 / 0.28 ( 3732) hydrogen bonds : bond 0.02320 / 1.41 ( 56) hydrogen bonds : angle 5.84680 / 4.00 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.122 Fit side-chains REVERT: C 38 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5600 (tp) REVERT: G 83 GLU cc_start: 0.8319 (tt0) cc_final: 0.8059 (tt0) REVERT: I 38 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5734 (tp) REVERT: L 38 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5657 (tp) REVERT: L 62 GLN cc_start: 0.8417 (mt0) cc_final: 0.8211 (mt0) REVERT: B 38 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5733 (tp) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.0585 time to fit residues: 4.2301 Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN G 62 GLN I 62 GLN E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.168869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129629 restraints weight = 2861.051| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.02 r_work: 0.3710 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2736 Z= 0.077 Angle : 0.418 3.430 3732 Z= 0.225 Chirality : 0.052 0.143 468 Planarity : 0.001 0.005 444 Dihedral : 33.087 179.805 486 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR L 39 PHE 0.010 0.002 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.08 ( 2736) covalent geometry : angle 0.41837 / 0.23 ( 3732) hydrogen bonds : bond 0.01595 / 0.99 ( 56) hydrogen bonds : angle 5.18473 / 3.56 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.122 Fit side-chains REVERT: G 83 GLU cc_start: 0.8344 (tt0) cc_final: 0.8115 (tt0) outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.0738 time to fit residues: 4.0569 Evaluate side-chains 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN L 79 GLN E 62 GLN B 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.166636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126708 restraints weight = 2826.726| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.00 r_work: 0.3659 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2736 Z= 0.101 Angle : 0.479 3.831 3732 Z= 0.256 Chirality : 0.053 0.160 468 Planarity : 0.001 0.005 444 Dihedral : 32.124 171.706 486 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR L 39 PHE 0.010 0.002 PHE L 94 HIS 0.003 0.002 HIS L 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 2736) covalent geometry : angle 0.47908 / 0.26 ( 3732) hydrogen bonds : bond 0.01642 / 1.01 ( 56) hydrogen bonds : angle 5.16816 / 3.59 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.113 Fit side-chains REVERT: G 83 GLU cc_start: 0.8389 (tt0) cc_final: 0.8138 (tt0) REVERT: L 61 GLU cc_start: 0.8481 (tt0) cc_final: 0.8040 (mt-10) REVERT: L 79 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8798 (tt0) outliers start: 6 outliers final: 1 residues processed: 45 average time/residue: 0.0745 time to fit residues: 4.0004 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.170185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129173 restraints weight = 2735.967| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.08 r_work: 0.3694 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2736 Z= 0.126 Angle : 0.494 3.393 3732 Z= 0.264 Chirality : 0.052 0.140 468 Planarity : 0.001 0.005 444 Dihedral : 31.785 170.532 486 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.59 % Allowed : 16.67 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 39 PHE 0.011 0.003 PHE L 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2736) covalent geometry : angle 0.49402 / 0.26 ( 3732) hydrogen bonds : bond 0.01692 / 1.01 ( 56) hydrogen bonds : angle 5.12398 / 3.56 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.116 Fit side-chains REVERT: G 83 GLU cc_start: 0.8306 (tt0) cc_final: 0.8080 (tt0) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.0696 time to fit residues: 3.8430 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.169529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128095 restraints weight = 2723.401| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.08 r_work: 0.3687 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2736 Z= 0.128 Angle : 0.498 3.365 3732 Z= 0.267 Chirality : 0.052 0.138 468 Planarity : 0.001 0.005 444 Dihedral : 31.102 172.169 486 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.96 % Allowed : 16.67 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR L 39 PHE 0.011 0.003 PHE L 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 2736) covalent geometry : angle 0.49751 / 0.27 ( 3732) hydrogen bonds : bond 0.01798 / 1.15 ( 56) hydrogen bonds : angle 5.15998 / 3.60 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.067 Fit side-chains REVERT: G 83 GLU cc_start: 0.8330 (tt0) cc_final: 0.8122 (tt0) outliers start: 8 outliers final: 8 residues processed: 45 average time/residue: 0.0667 time to fit residues: 3.6121 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN G 62 GLN G 79 GLN E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123171 restraints weight = 2725.534| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.11 r_work: 0.3611 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2736 Z= 0.198 Angle : 0.576 3.641 3732 Z= 0.308 Chirality : 0.053 0.133 468 Planarity : 0.002 0.008 444 Dihedral : 31.190 171.720 486 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.07 % Allowed : 15.93 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.013 0.003 PHE L 94 HIS 0.004 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 2736) covalent geometry : angle 0.57595 / 0.31 ( 3732) hydrogen bonds : bond 0.02120 / 1.26 ( 56) hydrogen bonds : angle 5.36071 / 3.75 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.108 Fit side-chains REVERT: G 83 GLU cc_start: 0.8374 (tt0) cc_final: 0.8149 (tt0) REVERT: L 61 GLU cc_start: 0.8549 (tt0) cc_final: 0.8262 (mt-10) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.0658 time to fit residues: 3.7822 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN L 62 GLN E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.168927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127773 restraints weight = 2768.677| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.08 r_work: 0.3678 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2736 Z= 0.121 Angle : 0.505 4.687 3732 Z= 0.269 Chirality : 0.052 0.140 468 Planarity : 0.001 0.006 444 Dihedral : 30.694 171.797 486 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.96 % Allowed : 17.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.011 0.003 PHE L 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 2736) covalent geometry : angle 0.50457 / 0.27 ( 3732) hydrogen bonds : bond 0.01680 / 1.02 ( 56) hydrogen bonds : angle 5.12313 / 3.57 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.119 Fit side-chains REVERT: G 83 GLU cc_start: 0.8356 (tt0) cc_final: 0.8150 (tt0) REVERT: L 61 GLU cc_start: 0.8526 (tt0) cc_final: 0.8229 (mt-10) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.0714 time to fit residues: 4.0349 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.0570 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.167382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125509 restraints weight = 2805.671| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.09 r_work: 0.3643 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2736 Z= 0.155 Angle : 0.537 3.433 3732 Z= 0.288 Chirality : 0.052 0.134 468 Planarity : 0.002 0.006 444 Dihedral : 30.513 171.690 486 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.07 % Allowed : 15.56 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.011 0.003 PHE L 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 2736) covalent geometry : angle 0.53711 / 0.29 ( 3732) hydrogen bonds : bond 0.01862 / 1.12 ( 56) hydrogen bonds : angle 5.18822 / 3.64 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.109 Fit side-chains REVERT: C 61 GLU cc_start: 0.8393 (tt0) cc_final: 0.8028 (mt-10) REVERT: G 83 GLU cc_start: 0.8390 (tt0) cc_final: 0.8181 (tt0) REVERT: L 61 GLU cc_start: 0.8559 (tt0) cc_final: 0.8283 (mt-10) outliers start: 11 outliers final: 11 residues processed: 49 average time/residue: 0.0664 time to fit residues: 3.9140 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.167477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125415 restraints weight = 2761.361| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.11 r_work: 0.3641 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2736 Z= 0.169 Angle : 0.559 3.788 3732 Z= 0.300 Chirality : 0.052 0.132 468 Planarity : 0.002 0.008 444 Dihedral : 30.422 171.055 486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.81 % Allowed : 14.81 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.012 0.003 PHE L 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 2736) covalent geometry : angle 0.55852 / 0.30 ( 3732) hydrogen bonds : bond 0.01945 / 1.17 ( 56) hydrogen bonds : angle 5.24790 / 3.68 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.100 Fit side-chains REVERT: C 61 GLU cc_start: 0.8239 (tt0) cc_final: 0.7799 (mt-10) REVERT: G 83 GLU cc_start: 0.8378 (tt0) cc_final: 0.8144 (tt0) REVERT: L 61 GLU cc_start: 0.8554 (tt0) cc_final: 0.8285 (mt-10) outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.0608 time to fit residues: 3.7207 Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN G 79 GLN L 62 GLN E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.164070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121772 restraints weight = 2752.947| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.13 r_work: 0.3597 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2736 Z= 0.250 Angle : 0.641 4.722 3732 Z= 0.342 Chirality : 0.053 0.130 468 Planarity : 0.002 0.009 444 Dihedral : 30.800 169.756 486 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.44 % Allowed : 15.56 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.014 0.003 PHE L 94 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 ( 2736) covalent geometry : angle 0.64062 / 0.34 ( 3732) hydrogen bonds : bond 0.02346 / 1.36 ( 56) hydrogen bonds : angle 5.43154 / 3.80 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 983.83 seconds wall clock time: 17 minutes 32.51 seconds (1052.51 seconds total)